NFL Nation: Jed York

SEATTLE -- Just throwing this out there, but if the San Francisco 49ers are not going to bring Jim Harbaugh back as head coach next season, why not pull the plug now and let, say, defensive line coach Jim Tomsula finish things out, as he did for one game in 2010?

Harbaugh
The 49ers, at 7-7 and officially eliminated from the NFC playoff race with Sunday’s 17-7 loss in Seattle, have nothing to play for but pride their final two games, home contests against the San Diego Chargers and Arizona Cardinals.

Because if Harbaugh will not be back to finish his five-year, $25 million contract in 2015 and he is seen as a lame duck the last two weeks, might that be even more of a distraction in the 49ers’ locker room?

"We’ve got two games left against two very good teams and we could worry about [Harbaugh] and get blown out the next two games and end the season on a sad note," said linebacker Michael Wilhoite. "Or we can not worry about it and just keep playing good football and fight and see what comes.

"We’ve got to ignore everything you guys say and everything the outsiders are saying. Keep it in-house and just keep fighting."

Easier said than done.

Harbaugh himself said he expects to have a conversation with Jed York and Trent Baalke about his future with the 49ers.

"I’m always available to sit down with the owner or general manager, absolutely," Harbaugh said.

The 49ers announced Sunday night that Harbaugh’s regular Monday media conference would occur as normal, at 12 noon PT.

The uncertainty surrounding Harbaugh has his quarterback flummoxed.

"It is not something I can fully wrap my mind around, why that would be the situation," Colin Kaepernick said of Harbaugh potentially being shown the door in Santa Clara. "But he has my full support, no matter if he is here or somewhere else.

"I hope he is back here, and I think he is a great coach."
In an Insider piece, ESPN analyst Louis Riddick looks at whether the San Francisco will and should extend the deal of quarterback Colin Kaepernick this offseason or wait until after his contract expires after 2014 season.

Jones
Kaepernick
Riddick makes some interesting points. But by hearing the words of the 49ers’ brass this week at the NFL owners meetings, the decision has been made.

The 49ers want to secure Kaepernick as soon a possible. In fact, on Tuesday, San Francisco general manager Trent Baalke said the team hopes to get a deal done for Kaepernick by the time training camp starts in late July.

It was significant because it was the first time the team put a timeline on the negotiations and it signified the team has seen enough -- they want him for the long term. Coach Jim Harbaugh and CEO Jed York echoed Baalke’s thoughts this week.

This is what Harbaugh said Wednesday morning, via ESPN Jacksonville Jaguars reporter Mike DiRocco: “I think we all know what Colin’s earning potential is. We all pretty much know what the numbers are … We all look at it that way. He deserves that. That’s what he deserves. That’s what the market pays for that job. Nobody attacks it more than he does. Nobody wants to be great like he does.”

That means the 49ers are preparing to pay Kaepernick a long-term deal that will likely average, at least, $18 million a year. It is a load of money, but Kaepernick is going into this season set to make just above $1 million. The kid is 21-18 as a starter and he has been to two NFC Championship games and a Super Bowl in less than two seasons as a starter.

Quarterbacks get paid. Kaepernick is an upper level quarterback and he deserves to be paid like it. It looks like it’s going to happen sooner rather than later.
Jim HarbaughChristian Petersen/Getty ImagesJim Harbaugh has reached the NFC title game in each of his three seasons, so why would the 49ers look elsewhere?

Coach Jim Harbaugh's situation in San Francisco has been one of the most talked-about stories in the league in recent weeks.

If a resolution on his contract isn't reached, it will likely hover over the franchise all season and would be a major story next January, when Harbaugh could leave the team, although Harbaugh told Sports Illustrated this week he is happy with all aspects of his job and doesn’t see any way he will leave the team before the end of his contract. Still, getting the contract done would ease a lot of issues.

We all know the backdrop: Harbaugh has led the 49ers to the NFC title game in all three of his seasons as coach. He got them to the Super Bowl after the 2012 season. He is entering the fourth year of a five-year contract that pays him $5 million per year. Harbaugh and the 49ers have been in discussion about a new deal for about a year, but are not close to an extension. Team owner Jed York recently told the Sacramento Bee he thinks contract talks will resume after the NFL draft in early May.

Things got interesting when the Cleveland Browns pursued a trade for Harbaugh. The 49ers were not interested, but that could change next year.

There have been rampant reports that Harbaugh has had trouble with some in the 49ers' front office, including general manager Trent Baalke. York, Harbaugh and Baalke have long downplayed the friction, indicating that they can coexist.

However, there is enough smoke here to think this situation go could south if a contract isn't agreed upon this year. Let's look at some issues that may be part of this story as it further develops:

The history: While it would be stunning to see the 49ers-Harbaugh marriage disintegrate after such a stellar start, similar breakups have happened before.

[+] EnlargeJimmy Johnson and Jerry Jones
AP Photo/Ron HeflinJim Harbaugh would not be the first successful coach to leave during a team's prime. Jimmy Johnson left the Cowboys after winning two Super Bowls because of fighting with owner Jerry Jones.
After winning two straight Super Bowls, Jimmy Johnson famously left the Cowboys in 1994 after fighting with owner Jerry Jones. Following the 1998 season, Mike Holmgren shocked the NFL when he left quarterback Brett Favre and a Green Bay Packers team in its prime after a seven-year run that included a Super Bowl win. Holmgren left for more power and much more money in Seattle. In 2002, the Raiders traded coach Jon Gruden to Tampa Bay for a massive amount of draft picks. The Raiders were burned as Gruden led the Buccaneers to a Super Bowl win against Oakland in his first season. In 2007, the Chargers sided with general manager A.J. Smith in his feud with coach Marty Schottenheimer even though the Chargers went 14-2 the season before.

If Harbaugh leaves the 49ers, it wouldn't be the first time a coach and team split despite success.

The highest-paid coaches: Harbaugh told Sports Illustrated he is not unhappy with his pay, but the man is underpaid considering his massive NFL success. Nine of the 32 NFL coaches in 2013 made at least $7 million. Only five of them had won a Super Bowl.

I'd think it has to bother Harbaugh that Chip Kelly earned $6.5 million in his first NFL season and NFC West rival Jeff Fisher made $7 million in St. Louis. Coaches' salaries are at a premium and, by NFL standards, Harbaugh is underpaid.

The best coaches without power: He is hypercompetitive and likes to be in control. So, Harbaugh probably isn't always thrilled to defer personnel decisions to Baalke. But I don't sense Harbaugh wanting to be the general manager and making every decision as he said. He is a coach.

I don't see this as a deal-breaker.

There are plenty of great NFL coaches who don't have total power, including Harbaugh's brother, John, in Baltimore. There's also Mike McCarthy in Green Bay, Mike Tomlin in Pittsburgh and Pete Carroll in Seattle. So, a lack of total power in the NFL really isn't a big deal anymore for coaches.

[+] EnlargeDavid Shaw
AP Photo/Matt YorkWould Stanford coach David Shaw be a candidate to follow Jim Harbaugh again?
Where could Harbaugh land? Harbaugh's situation could cause teams to adjust their plans late in the season. I could see many owners prematurely firing a coach to get a shot at Harbaugh if he goes into January unsigned.

But right now, the list of teams that may be making a change next year and may make sense for Harbaugh isn't very long.

Miami and Dallas would be among the biggest suitors. Miami tried to hire Harbaugh before he went to San Francisco. The team has deep pockets, a need for good public relations, and the Dolphins have a good young quarterback in Ryan Tannehill. Dallas has big bucks and Tony Romo. Harbaugh could like both places.

Other possibilities could include both New York teams and Atlanta (coaching Matt Ryan would surely be intriguing). A potential long shot could be Oakland. Harbaugh was an assistant in Oakland and he could stay in the Bay Area. But the Raiders have to find a quarterback and ownership would have to be willing to shell out financially to make it work. Plus, the 49ers would need to get a haul from the Raiders to trade him to their Bay Area rival.

If I had to give odds on the early favorite, I'd look toward Miami.

Who could replace Harbaugh? It's only logical to think that San Francisco ownership, in the back of its mind, is thinking post-Harbaugh just in case.

The chance of getting draft picks for a coach the 49ers can't come to an agreement with could interest the team next offseason. Also, the idea of front-office peace could be at the forefront as well, especially if things go haywire the rest of this year.

The first place the 49ers would likely look to replace Harbaugh is on the current staff. Because the team has been so successful, I could see the 49ers having interest in staying close to home. Offensive and defensive coordinators Greg Roman and Vic Fangio, respectively, would likely be on the 49ers' list. Defensive line coach Jim Tomsula is a favorite of the front office. He was a candidate when Harbaugh was hired and his players love him.

Here's another name the 49ers could look at -- David Shaw. He replaced Harbaugh at Stanford. I'm sure he wouldn't be afraid to do it again.

Shaw has been steadfast in his desire to stay at Stanford. But if he were ever to leave for the NFL, this would likely be an appealing situation. He and his family could stay in their house and he'd go to a near perfect NFL situation with a franchise quarterback in Colin Kaepernick.

There is plenty to unfold in this situation in the next several months. Harbaugh and the 49ers could end it all by coming to a contract extension. But as we have realized early this offseason, it's not that simple.
I've spent the day in meetings at ESPN headquarters.

As I catch up on the day's events, I am not surprised by the primary topic: Yes, the Jim Harbaugh situation. As I wrote in a previous post, this type of attention is to be expected after a bombshell story such as the one involving the Cleveland Browns' interest in Harbaugh that surfaced Friday.

Harbaugh
All the speculation about Harbaugh's issues with the 49ers' front office have bubbled up to the surface.

Perhaps closing out the Cleveland portion of this tale (I have a feeling, though, the Harbaugh story is far from over) 49ers' owner Jed York told the Sacramento Bee that the Browns had interest and the 49ers quickly scuttled talks. That is in line with what I've heard all along.

Look, we all review the film of our decisions, but I think the 49ers may regret not initially telling their side of the story Friday. It could have quickly ended the talk.

The most intriguing aspect of the York interview with The Bee was that he said he expects contract talks with Harbaugh to resume after the May draft. I guess there is no hurry to do it, but a deal must get done this calendar year or Harbaugh's future will be a feeding frenzy next year as teams try to make a deal for him entering his final season.

Meanwhile, the Harbaugh-49ers saga is now Topic A in the NFL. Hey, it's February. Juicy talk rules.

Here are some topics for your 49ers' hand-wringing pleasure:

ESPN's Ashley Fox believes the 49ers' success starts with Harbaugh. He has led a team that was irrelevant before he got there to three straight NFC title games.

ESPN Insider Mike Sando thinks the draft is the key for the 49ers to continue to their success Insider.

Grantland's Bill Barnwell tries to make sense of the entire saga.

In other 49ers' related-news:

Backup safety Craig Dahl took a $600,000 pay reduction to stay with the team. It has been in the works for several days. The open big remaining pay-cut question is cornerback Carlos Rogers. The team is not expected to pay his $6 million salary. If he doesn't take a large pay cut he will likely be released.

Jim Harbaugh denies trade report

February, 22, 2014
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San Francisco 49ers coach Jim Harbaugh backed up the denial of team owner Jed York about his near-made reported trade to Cleveland for a package of draft picks in a text to ESPN's Ed Werder.

Harbaugh wrote this to Werder: "I echo Jed York's comment ... 'isn't true.' I know nothing about a trade with the Cleveland Browns and us, involving me."

Friday, York tweeted this: Report isn't true.

ESPN's Chris Mortensen confirmed the Pro Football Talk that the Browns' pursuit reached a serious point. But such a trade would take total cooperation by all sides and obviously it never happened.

My thoughts remain the same. The story doesn't matter. What only matters now is that the 49ers and Harbaugh iron out any rough spots in their relationship and agree on a contract extension. The two sides are good for each other and are only set up for more success.

Meanwhile, the NFL Network reported the 49ers had preliminary talks with the agent of quarterback Colin Kaepernick at the NFL combine. That was expected. The two sides will discuss a long-term deal over the next several months. Kaepernick is entering the final season of his rookie contract, but the team can give him the franchise tag next year.

The report that the San Francisco 49ers discussed a deal to send coach Jim Harbaugh to Cleveland for a package of draft picks really doesn't matter anymore.

It didn't happen. It won't happen.

49ers owner Jed York responded on twitter that the Pro Football Talk report is not true.

Whether or not the story is true, this isn't the first time there has been talk of issues between Harbaugh and the team. There have been reports of occasional professional tension between Harbaugh and general manager Trent Baalke. Contract extension talks have been unsuccessful thus far. The two sides have discussed a deal for a year, yet nothing has happened. Harbaugh enters the fourth year of a five-year deal.

Harbaugh wants top dollar, but the 49ers want to see him win a Super Bowl first.

Harbaugh -- who has led the 49ers to the NFC title game in each of his three seasons as an NFL coach -- was also connected to the University of Texas job late last season. These types of things will continue to happen unless there is a contract extension.

However, I believe this situation will get resolved. Harbaugh and the 49ers can and will co-exist.

The report stated the coach didn't want to leave the 49ers. He knows this is the best place for him. The 49ers have one of the best rosters in the NFL and he loves coaching quarterback Colin Kaepernick. He also knows 26-year-old franchise quarterbacks are rare.

The 49ers, who if Harbaugh did leave would likely strongly consider prompting defensive line coach Jim Tomsula to head coach, also know Harbaugh is special. This five-time Super Bowl-winning franchise was had become all but irrelevant before Harbaugh was hired.

They are moving into a new stadium this year. They want Harbaugh to be part of it for now and the foreseeable future. No matter what a potential trade would have brought, I think the 49ers would have lost.

They don't need more draft picks. They need strong coaching.

The only way of ensuring it is getting an extension for Harbaugh done. If the 49ers can't, this story about a trade with Cleveland will have legs and hover over the team. Undoubtedly, it will create future angst and further stories.

If we get to December and Harbaugh is still months away from his walk year, there will be a lot of teams looking to make a splash in 2015 and ready to make a big trade for Harbaugh.

That will not be good for the franchise. The 49ers have a great thing going and Harbaugh is a big reason why. Getting an extension is the only smart solution to ensure stories like this go away.
SANTA CLARA, Calif. – It appears the San Francisco 49ers will travel to Tampa Bay at near full health.

The biggest injury question is whether left guard Mike Iupati will return from a sprained knee. He’s missed the past three games. He has practiced on a limited basis all week. 49ers coach Jim Harbaugh said Friday it’s possible that Iupati can play Sunday. If he can’t, Adam Snyder will make his fourth straight start.

Receiver Michael Crabtree is probable with an ankle injury that he tweaked against Seattle last week. Crabtree suffered the injury early and he finished the game. He practiced all week.

In other notes:

49ers CEO Jed York playfully tries to budge Seattle quarterback Russell Wilson to the diamond.

In an Insider piece, Pro Football Focus ranksInsider the 49ers as the 12th-deepest roster. I disagree. This team is loaded. It’s a top-five roster, in my opinion.

Would Jim Harbaugh leave the 49ers?

December, 12, 2013
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SANTA CLARA, Calif. – Get used to this.

Several reports, including from ESPN’s Chris Mortensen, have suggested that the University of Texas will include Jim Harbaugh on its list of candidates once Mack Brown is out as coach.

The San Francisco 49ers’ wildly successful third-year coach was asked about it at his news conference Wednesday. He said: “I don’t ever talk about any jobs other than the one I have.”

Don't read too much into the response. That’s his standard answer. It doesn’t mean he is interested in Texas. It doesn’t necessarily mean he isn’t, either.

[+] EnlargeJim Harbaugh
Thearon W. Henderson/Getty Images"I don't ever talk about any jobs other than the one I have," 49ers coach Jim Harbaugh said. But that may not keep Texas and others from pursuing him.
Would Harbaugh leave the Bay Area for Austin?

Never rule anything out. Everything is on the table. But I would be surprised if Harbaugh left the 49ers right now.

At the same time, this probably won't be the last time Harbaugh is connected to another job. It will happen every year. Such annoyance comes with employing a coach with a great reputation. Others want to see if they can snare him. NFL teams by rule can’t touch him yet, but colleges can. Thus, it makes sense that a school with deep pockets, like Texas, might consider Harbaugh.

Again, hard to say with confidence that the job wouldn't appeal to him. The compensation that has been connected to this job is insane. Anyone the school contacts would be silly not to listen. But even if the Longhorns put on the full-court press, I don’t know if Harbaugh would leave.

He seems to be happy with the 49ers and in the Bay Area. He knows he has a great thing going with a strong roster, a young quarterback and a new stadium coming in 2014, not to mention a loyal fan base and an ownership that wants to keep winning. Who’s to say the 49ers don’t have it better than the University of Texas?

Harbaugh is famous for his competitive nature. I’m not so sure he would leave the NFL at this point, especially after he lost the Super Bowl to his brother’s team in just his second season as a pro coach. Harbaugh is a former NFL quarterback. He knows the lure of a Super Bowl ring. I can’t see him stopping that chase while with a team that should be in the hunt for the next several years.

Remember, when Harbaugh was at Stanford he turned down a chance to coach at his alma mater, Michigan, to go to the NFL. Why would he want to leave the NFL now when he has it so good?

This interest will only help Harbaugh, though. There has been talk for months of a contract extension. He is in the third year of a five-year, $25 million deal. Just the thought of Harbaugh leaving the Bay Area for burnt orange is probably causing 49ers owner Jed York to reach for his wallet.

Harbaugh is invaluable to the 49ers. The franchise, which won the last of its five Super Bowl championships almost two decades ago, wants to be elite again. They saw their fortunes turn around when Harbaugh made the short drive from Stanford less than three years ago. They couldn’t bear to watch him leave, especially with everything else in place.

I’m sure the 49ers will use this opportunity to show Harbaugh how much he means to the franchise. Will it be enough? I would think so, yes, as it seems like Harbaugh has everything he wants. But that doesn’t mean the outside interest will stop if he doesn’t go to Austin.
Colin KaepernickAP Photo/Mark ZaleskiColin Kaepernick rushed for a season-high 68 yards on 11 carries against the Titans.
NASHVILLE -- San Francisco 49ers CEO Jed York was all smiles as he casually hung out in the victorious locker room Sunday night. He watched his players get ready for a nine-hour flight to London, where English fans will be treated to one of the hottest teams in the NFL.

It was a stark difference from the last time York was in the 49ers locker room. After a loss to the Indianapolis Colts on Sept. 22, York spoke glumly to the media about star pass-rusher Aldon Smith leaving the team for an alcohol treatment center. The loss dropped the 49ers to 1-2 (the first time the team lost back-to-back games under coach Jim Harbaugh) and they were beaten by the Seattle Seahawks and the Indianapolis Colts by a combined score of 56-10.

The defending NFC champions were in a crisis and it appeared the season could be unraveling.

Fast-forward four weeks and that moment appears a distant memory. The 49ers' rebirth continued with an impressive 31-17 win at the Tennessee Titans on Sunday. The 49ers have won four straight games, scoring more than 30 points in each. It's the first time since 1998 San Francisco has accomplished that feat.

“We feel pretty good about what we are doing right now,” said quarterback Colin Kaepernick, who had his most effective game of the season as a runner Sunday.

There is no reason to think the 49ers will not continue their roll. They play the 0-7 Jacksonville Jaguars on Sunday in London. Yes, it’s an any-given-Sunday league, but Harbaugh’s team seems upset-proof. The 49ers should go into the bye week -- and the midseason point -- at 6-2.

Teams hope to go 3-1 every quarter of the season to get to 12-4. At 1-2, 12-4 looked like a difficult feat for San Francisco. Now it seems quite possible for the 49ers, who trail Seattle (6-1) by a game in the NFC West.

Credit goes to the organization for responding to the adversity after Week 3.

It starts with Harbaugh and his staff. It was the first difficult moment Harbaugh had in his tenure in San Francisco, which started in 2011. He and his staff handled it beautifully. In fact, the day after the Colts game, Harbaugh said he relished the opportunity to face adversity and to “whip it.” So far he and his team are beating adversity on all three scorers’ cards.

San Francisco left tackle Joe Staley said the key to bouncing back was sticking together.

"The sky wasn’t falling,” Staley said. “No one was pointing fingers at each other … We stayed together.”

And it continues to get better.

In some ways, Sunday’s win was the most impressive of the season. Tennessee is good at home and has a strong defense. But the 49ers completely owned this game.

The 49ers led 24-0 going into the fourth quarter and shut down Tennessee in all three phases of the game.

The San Francisco defense hasn’t missed a beat since Smith left the team for substance abuse treatment 27 days ago. The 49ers have allowed a combined 51 points in the past four games. San Francisco got two more turnovers Sunday and has forced 12 during the winning streak. The 49ers have turned each turnover into points -- they have eight touchdowns and four field goals after the turnovers.

While the San Francisco defense continues to dominate, the offense (which has been a work in progress without injured receivers Michael Crabtree and Mario Manningham) was dynamic Sunday.

According to ESPN Stats & Information, Kaepernick ran out of the read-option offense five times for 36 yards and a 20-yard rushing touchdown. Kaepernick had nine zone-read rushes for 14 yards this season coming into the game and ended up with 69 yards on 10 carries. He completed 13 of 21 passes for 199 yards. Kaepernick led the team to eight third-down conversions in 10 tries in the first half.

Kaepernick’s Total QBR was 99.0 out of a possible 100. It is the best mark in the NFL this season.

Will we see the 49ers use the read-option much in the immediate future? Probably occasionally. Harbaugh said it is a “club” in the team’s bag. Kaepernick said it was used because the Titans were giving the 49ers opportunities.

Still, it is also a sign things are working well. With Smith, Crabtree and Manningham all expected back at some point this season, the 49ers have the look of a team that is going to stick around for a while.

Four weeks ago, many may not have been confident in that possibility.

Floundering 49ers have big problems

September, 22, 2013
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Colin Kaepernick(AP Photo/Marcio Jose SanchezColin Kaepernick and the 49ers offense continue to struggle to move the ball.

SAN FRANCISCO -- Pick a problem. There are plenty from which to choose.

That is what is so worrisome for the San Francisco 49ers as they are under .500 for the first time under coach Jim Harbaugh. Yes, the 49ers are 1-2 and trail rival Seattle (3-0) by two games in the NFC West. It is early.

Still, the 49ers have real problems. After a deflating 27-7 home loss to the Indianapolis Colts on Sunday, the 49ers are dealing with poor offensive play, mounting injuries and Aldon Smith's off-field issues.

The problems are serious and the beleaguered defending NFC champions -- who have been outscored by a combined 56-10 the past two Sundays -- somehow have to find a way to rebound on short notice. The 49ers play at the St. Louis Rams on Thursday. The Rams tied and beat the 49ers last season.

San Francisco will also go forward without Smith, their star pass-rusher.

A quiet locker room became a serious one Sunday afternoon when Smith made his first public statement since being arrested at 7:02 a.m. Friday on charges of drunk driving and possession of marijuana. Smith vowed to “fix” his problem. Then, 49ers CEO Jed York said Smith is leaving the team indefinitely to deal with a personal matter. Smith is expected to check into a treatment center this week.

Often, alcohol treatment plans are for 28 days. Thus, the 49ers may be without one for the most dynamic pass-rushers in the NFL for the next month. Smith, who turns 24 on Wednesday, deserves credit for trying to get a handle on his personal life. However, star athletes don’t often leave their teams in season to get treatment. Smith’s situation will be closely watched around the league.

The 49ers -- who were dominated at home by an Indianapolis team that was playing without six injured starters -- have several pressing, more traditional football problems.

It starts with the offense. It is amazing to think the unit on the field Sunday was the same one that beat Green Bay in Week 1. In that game, quarterback Colin Kaepernick threw for 412 yards and receiver Anquan Boldin had 13 catches. The 49ers were dynamic offensively.

They were anemic Sunday against a Colts’ defense that is not known as a giant killer. Kaepernick threw for 150 yards. Most of it was in garbage time. He had two completions at halftime.

According to ESPN Stats & Information, Kaepernick was 1-for-6 on passes that traveled more than 10 yards down field. Last season, Kaepernick completed 55.6 percent of such throws. It was the fifth best in the NFL. This year, he is completing just 37.8 percent.

Kaepernick went from being jaw-dropping good against Green Bay to totally ineffective the past two games.

It was not all on Kaepernick. His receivers could not get open for the second straight week after being shut down in Seattle. That poor performance was chalked up to the Seahawks’ superior secondary. That cannot be said about the Colts’ secondary.

The 49ers have to do something about getting their receivers open. Boldin is fine, but he needs help. Mario Manningham (knee) may be back in a month and Michael Crabtree (Achilles) is hopeful to return late in the season.

Perhaps it is time San Francisco returns to the read-option offense in which Kaepernick had success last year. The team has used it sparingly this season. Offensive coordinator Greg Roman said last week that could change.

With the offense desperate for a spark, there’s no doubt the 49ers’ coaching staff will consider everything.

It did not help that star tight end Vernon Davis was out with a hamstring injury. Sunday was his first missed game in six years. There is no guarantee he will be ready to face the Rams. Inside linebacker Patrick Willis -- the heart and soul of the team -- left in the third quarter with a groin injury. He declined to speak to reporters after the game.

As the 49ers try to figure what has gone wrong so quickly, they know their issues run deep. A hole has been dug. According to ESPN Stats & Information, since 1990 only 24 percent of the teams that started 1-2 made the playoffs.

“It is a pivotal time of the season,” safety Donte Whitner said. “But the sky is not falling. … We need to deal with this adversity.”

NFL Week 3 Sunday Studs and Duds

September, 22, 2013
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Week 3 left us with fewer wrinkles and slightly longer fingernails. After 22 of the first 32 games this season were decided by fewer than eight points, the majority of Sunday's games were double-digit blowouts.

The New York Giants absorbed a 38-0 licking from the Carolina Panthers. It got so ugly at CenturyLink Field that the Seattle Seahawks played backup quarterback Tarvaris Jackson for the final 18 minutes, 54 seconds of their 45-17 victory over the Jacksonville Jaguars. And even one of the closer games, the New York Jets' 27-20 victory over the Buffalo Bills, wouldn't have been that close were it not for the Jets' team-record 20 penalties.

No further setup is needed for our weekly take on Sunday's best and worst performers:

STUDS

Richardson
1. The Trent Richardson trade, Cleveland Browns and Indianapolis Colts: The consensus analysis suggested that both teams won the trade that sent Richardson to the Colts for a first-round draft choice. For one week, at least, that analysis held up. The Browns let loose in an upset victory over Minnesota, scoring a touchdown on a fake field goal, setting up a field goal with a fake punt and letting new quarterback Brian Hoyer throw 54 times. The Browns looked like they were having too much fun to accept a tanking of the season; good for coach Rob Chudzinski and his staff. The Colts' acquisition of Richardson, meanwhile, paid off with a goal-line touchdown on his first carry and, more important, seemed to have inspired the presumably displaced Ahmad Bradshaw, who ran for 95 yards in the Colts' 27-7 victory over San Francisco.

Tannehill
2. Ryan Tannehill, Miami Dolphins quarterback: Tannehill didn't put up the raw yardage as he did in previous victories over the Browns and Colts, but his fourth-quarter performance Sunday against the Atlanta Falcons was special. He threw on 12 of the 13 plays on the Dolphins' game-winning drive, completing nine -- including twice on third down -- for 69 yards and a 1-yard touchdown pass to receiver Dion Sims. No one seems quite sure where to classify Tannehill among his fellow quarterbacks in the 2012 draft class, but at this point, we can't ignore his role in Dolphins' first 3-0 start since 2002.

3. Rush offense, Dallas Cowboys: It's certainly worth nothing that tailback DeMarco Murray gashed the St. Louis Rams for 175 yards in an easy 31-7 victory. But this is one of those occasions where the running back shouldn't get all the credit for a big day. According to ESPN Stats & Information, 149 of Murray's yards came before contact. That means the Cowboys did a smart job with their play-calling relative to the Rams' scheme. It also suggests that the Cowboys' blockers did an exceptional job of keeping defenders away from him. It usually takes more than one to get it done, as the kids like to say. (Or maybe they don't. I just made that up.)

Lewis
4. Marvin Lewis, Cincinnati Bengals coach: Lewis' team didn't make it pretty Sunday at Paul Brown Stadium, beating the Green Bay Packers despite committing turnovers on four consecutive possessions at one point. So as the Bengals' highlight, I'll pick out Lewis' sharp and, it turns out, critical catch of a poor spot on an apparent Packers first down late in the fourth quarter. Replays confirmed that receiver Randall Cobb's knee touched the ground before the ball crossed the line to gain the first down. On the ensuing fourth-down play, the Bengals forced a fumble and Terence Newman returned it for the game-winning touchdown. It wouldn't have happened without Lewis' challenge. Last season, Lewis didn't get a call reversed. He's already had two in 2013.

5. Defense, New Orleans Saints: Rob Ryan's overhaul of this group continues to impress. No one has scored more than 17 points against the Saints this season, matching the number produced by their 2012 defense over 16 games. Sunday, the Arizona Cardinals managed just one score and 247 total yards in the Saints' 31-7 victory. One of the most encouraging factors has been the play of rookie safety Kenny Vacarro, who broke up a potential game-deciding touchdown in Week 1 and had a fourth-quarter interception Sunday.

DUDS

1. Decision-making, San Francisco 49ers: The team allowed linebacker Aldon Smith to play Sunday against the Colts, two days after he was arrested on suspicion of driving under the influence. Immediately after the game, Smith and the team confirmed he would leave indefinitely to "get better," according to CEO Jed York. It was a weak sequence of events no matter how you look at it. Don't get caught up in whether the 49ers could have officially suspended him based on the NFL's collective bargaining agreement. And let's not worry about whether it would have been fair to discipline Smith, who is supposed to be innocent until proven guilty. If the situation is grave enough that Smith needs help away from the team, and assuming that decision was made before the game rather than in the 20 minutes between its conclusion and the announcement, then the 49ers made an indefensible decision to play him. If they were concerned about Smith's well-being, they could have made him a game-day deactivation and sent him to deal with his issues immediately rather than wait to squeeze one more game out of him.

Leavy
Leavy
2. Bill Leavy, NFL referee: Leavy and his crew made their second basic misapplication of a rule in three weeks. Sunday, Leavy overlooked the new wording of the so-called "Jim Schwartz rule" that penalizes coaches for challenging non-reviewable plays. In the second quarter at the Metrodome, Leavy penalized the Vikings 15 yards instead of docking them a timeout after coach Leslie Frazier challenged a fumble. (The rule was rewritten in the offseason.) Instead of getting the ball on the Browns' 26-yard line with two timeouts left, the Vikings faced a first-and-25 at the 41-yard line and eventually settled for a field goal. In Week 1, you might recall, Leavy rendered the wrong down after a Packers penalty and was also publicly contradicted on a personal foul he called by league vice president of officiating Dean Blandino. The NFL rule book is thick and nuanced, but Leavy is a veteran referee. You would hope his mistakes would be of judgment rather than of factual error.

3. Pass protection, New York Giants: There are so many places to spread blame when one NFL team loses to another by a score of 38-0. The NFL deck is heavily stacked against such outcomes, and blame for the Giants' embarrassing performance Sunday can be spread evenly. But I'll focus my angst at the team's pass-protection schemes, which allowed six -- yes, SIX!!! -- sacks in the first 17 minutes of "action" against the Panthers. Manning took seven sacks in the game before the Giants mercifully put in backup Curtis Painter. The Giants are now 0-3 for the first time since 1996 and growing less competitive by the week.

Frazier
4. Leslie Frazier, Minnesota Vikings coach: Recent history (since 1990) tells us the Vikings have a 3 percent chance of making the playoffs after starting 0-3. But that's only part of the concern for Frazier, who got outcoached by the legendary guru across the field (Chudzinski) in his home opener. The Vikings fell for two trick plays on special teams, and for the second consecutive week their defense was helpless on a game-winning drive. Worse, Frazier's errant challenge flag was compounded by his apparent failure to point out Leavy's mistake. Remember, Frazier is essentially in a contract year. It has been assumed he needs a playoff appearance to get a new deal. The Vikings' meager chances of a postseason berth suggest that Frazier is in his final months as the team's coach.

Jones
Kaepernick
5. Colin Kaepernick, San Francisco 49ers quarterback: Only a late surge of garbage yards got Kaepernick over the 100-yard mark against the Colts. He still completed fewer than 50 percent of his passes, took three sacks and finished with an 11.8 Total QBR. Worse, Kaepernick looked hesitant and especially unsure of whether he should run or keep looking downfield for receivers. It's true that tight end Vernon Davis didn't play, and a depleted receiving corps contributed to just one completion on passes that traveled at least 10 yards downfield. But anyone who watches Kaepernick regularly would accept that he is in the first slump of his young career.
SAN FRANCISCO -- Observed in the locker room after the San Francisco 49ers27-7 loss to the Indianapolis Colts:

Smith
Surreal scene: The 49ers were pounded for the second straight game, but the focus was on embattled pass-rusher Aldon Smith. He made a statement to the media after the game, his first public words since he was arrested Friday morning on suspicion of driving under the influence and marijuana possession.

"I apologize to the team and the organization," Smith said. "This is something that I will get fixed. I will do everything in my power to make sure this never happens again."

Smith is expected to receive treatment for substance abuse. 49ers CEO Jed York said Smith will not be with the team Thursday in St. Louis, and he will be away indefinitely.

"I believe Aldon wants to tackle this problem, and we’re going to do everything we can do to help him with this," York said. "I am willing to support Aldon as long as he is willing to work at this and fight to get better."

Willis injured: Star linebacker Patrick Willis declined to talk after the game. He left in the third quarter with a groin injury. The team did not announce the severity of the injury.

Turning point: Safety Donte Whitner acknowledged that the team has reached a pivotal point in the season but added that the “sky is not falling.”

Whitner was hit with a 15-yard penalty for using the crown of his helmet on the first offensive play of the game. It helped lead to a Colts touchdown. Whitner said he led with his shoulder and that any big hit in the NFL these days is going to result in a penalty.
video
The Super Bowl is coming to the San Francisco 49ers' new stadium in 2016, the latest victory for the organization.

The announcement, delivered by the NFL on Tuesday, was expected because South Florida's efforts had faltered. That should not diminish the moment for San Francisco or the 49ers.

Count this as another sign of progress for the team under chief operating officer Jed York. The recent scorecard includes:
  • Hiring Baalke as GM: Hiring Trent Baalke as general manager didn't seem like a bold move at the time. Baalke had been working in the organization for years. The organization had slipped somewhat during that time. However, Baalke played a role in landing the right coach, and he has blossomed as a first-time GM. Maximizing the draft and trades related to the draft appear to be one specialty.
  • Getting Harbaugh as coach: Baalke's hiring precipitated Jim Harbaugh's hiring as coach for the 2011 season. Harbaugh's immediate success validated the personnel work Baalke and former GM Scot McCloughan had done in building the roster. As a bonus, they landed a hot candidate without giving him a GM-type role.
  • Drafting a franchise QB: Colin Kaepernick played a leading role in getting the 49ers to the Super Bowl last season, less than two years after Baalke and Harbaugh used a second-round pick to select him.
  • Finding an elite pass-rusher: Aldon Smith's selection as the seventh overall choice in the 2011 draft was not a widely anticipated move. Mock drafts generally were not projecting Smith to go to the 49ers. The move has been a home run so far. Smith had 19.5 sacks last season.
  • Two division titles: The 49ers have won the past two NFC West titles.
  • Super Bowl appearance: The 49ers advanced to the Super Bowl in Harbaugh's second season, a first for the organization since the 1994 season.
  • Securing a new stadium: Candlestick Park has a rich history, but no future. Teams have struggled mightily to get new stadiums built in California. The 49ers made it happen.
  • Selling naming-rights deal: The 49ers reached a $220.3 million stadium naming-rights deal with Levi Strauss & Co. The deal will help pay down the stadium debt.
  • Securing Super Bowl: Teams building new stadiums in areas with relatively moderate climates fare pretty well in securing Super Bowls. Still, there were no guarantees for the 49ers. They partnered with local leaders to win the bid.

OK, enough praise for one team in one post. Let's get back to mocking one another in the comments section. I'll kick it off by asking, "Which NFC West team is most likely to represent the NFC in the 49ers' new stadium?"

Two strong takes on Chris Culliver

January, 31, 2013
1/31/13
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NEW ORLEANS -- The media throng awaiting San Francisco 49ers cornerback Chris Culliver in the team hotel Thursday caught some teammates by surprise. Amazed looks crossed their faces as they arrived for the final full-team media session before Super Bowl XLVII.

Culliver
The massive fallout from Culliver's anti-gay remarks earlier in the week threatens to distract him from his work in the game Sunday. The fallout has already forced coach Jim Harbaugh and others in the organization to redirect resources toward a response plan. As Harbaugh suggested Thursday, the fallout could affect Culliver's long-term standing on the team.

LZ Granderson of ESPN.com and Ray Ratto of CSNBayArea.com have offered strong takes on the subject.

Granderson criticized Culliver for "hiding behind statements co-authored by other people" after the 49ers issued the following prepared statement from Culliver:
"The derogatory comments I made yesterday were a reflection of thoughts in my head, but they are not how I feel. It has taken me seeing them in print to realize that they are hurtful and ugly. Those discriminating feelings are truly not in my heart. Further, I apologize to those who I have hurt and offended, and I pledge to learn and grow from this experience."

The statement was obviously prepared by public-relations professionals. The 49ers weren't going to let Culliver issue his own statement. This was an initial attempt at damage control. Culliver will have to do much more of the work in the future to become credible.

Ratto suggests Culliver's offending remarks resonated through the highest levels of the 49ers' organization in a manner that threatens Culliver's standing with the team. He points to the embarrassment team owner Jed York must have felt.

"As someone who has been on the forefront of anti-gay bullying action in the NFL, [York] had to spend his Thursday grappling with L’affaire Culliver rather than basking in the reflected glory of his team," Ratto wrote.

Not quite two weeks ago, Culliver's interception off Matt Ryan in the NFC Championship Game helped the 49ers defeat the Atlanta Falcons, 28-24. Afterward, Culliver excitedly explained how the 49ers had adjusted to the Falcons' bunch formations after falling behind.

Culliver has played more than 75 percent of the 49ers' defensive snaps in the playoffs. He's a big part of the 49ers' defensive plan against Baltimore and a bigger question mark moving forward.
Aldon Smith Kevin C. Cox/Getty ImagesAldon Smith and San Francisco's defense got to Matt Ryan in the second half.

ATLANTA -- There was so much for the San Francisco 49ers to celebrate Sunday following their 28-24 victory over the Atlanta Falcons in the NFC Championship Game.

A couple of the younger players, Ricky Jean Francois and Anthony Dixon, danced on a riser at the far end of the 49ers' locker room.

Team owner Jed York, brought up around the 49ers when his legendary uncle was running the team, teared up while explaining how his own son, 3-month-old Jaxon Edward, had calmed his nerves during a rough first quarter.

But the only NFL franchise with a 5-0 record in Super Bowls won't go into full celebration mode without claiming one more victory.

Let's get that part straight right away.

"We have one more to go and we know that," York said.

Some of the players were too tired to celebrate, anyway. They had fallen behind 17-0 after 16 minutes, trailed 24-14 at the half and needed their defense to hold on fourth-and-4 from its own 10-yard line with 1:13 to play.

"It was tense as hell at the end," left tackle Joe Staley said.

Staley captured the feeling as the 49ers tried to process what had delivered them to their sixth Super Bowl appearance and first since the 1994 season, when some of them were in elementary school and York, now 31, was not yet eligible for driver's ed. Staley, usually quick with a quip, leaned against his locker and struggled to explain how the team had recovered from a 42-13 defeat at Seattle in Week 16 to post its first three-game winning streak of the season.

"I'm not full of quotes right now," Staley said. "I'm just tired."

The 49ers now have two weeks to prepare for their Super Bowl matchup against the Baltimore Ravens. They'll take every additional day they can get after prevailing in a game they had to survive before they could win.

The 49ers have built their identity on defense for years, but Colin Kaepernick's emergence at quarterback was changing the dynamic.

Kaepernick was again outstanding Sunday, completing 76.2 percent of his passes for 233 yards with one touchdown, one sack, no turnovers and a 127.7 NFL passer rating. A week after setting an NFL record for quarterbacks with 181 yards rushing, Kaepernick carried just twice for 21 yards against the Falcons. He remained in the pocket on 21 of 23 drop backs and averaged 11.5 yards per pass attempt when throwing from there.

The 49ers can win a championship with that type of quarterback play.

Yet, for as effective as Kaepernick was passing the ball after a dismal first quarter, the 49ers would not have won this game without two elements they had counted on for years in the absence of a viable passing game: a ground game led by Frank Gore and an opportunistic, physical defense.

Gore carried 21 times for 90 yards and two scores. The pass protection he provided was also critical on a throw Kaepernick completed to Vernon Davis for 25 yards to the Atlanta 4. Gore and LaMichael James combined for three touchdowns on option plays. Kaepernick, who had seven option rushes for 99 yards against Green Bay, handed off all 13 times on options against Atlanta.

Gore remained in full uniform at his locker after most of his teammates had showered and dressed. He cited interview requests as the reason, but if Gore wanted to savor the moment after eight mostly rough seasons with the team, he was entitled to that, as well.

"Came out of college and had knee injury after knee injury, but kept fighting," Gore said. "Same as this team. We kept fighting from '05 to now, being the laughed-at team in the league to one of the best. It feels great."

The 49ers' defense had been less consistent late in the season as injuries sidelined Pro Bowl end Justin Smith while slowing pass-rusher Aldon Smith. Having a bye in the wild-card round was critical to the defense regaining its footing for the Green Bay Packers. Having an extra week before the Super Bowl feels necessary again after the 49ers chased Julio Jones and the Falcons' receivers all over the Georgia Dome, with mixed results.

"It's definitely good for the body," Aldon Smith said.

The 49ers had trouble pressuring Falcons quarterback Matt Ryan until late in the game. Their secondary initially struggled matching up against the Falcons' bunch formations. That combination -- not enough pressure up front, too much confusion in the back -- enabled Ryan to pass for 271 yards and three scores in the first half. Jones had 100 yards through one quarter and 182 for the game.

Cornerback Chris Culliver and strong safety Donte Whitner said the 49ers had trouble getting their hands on the receivers early in the game. The Falcons used those bunch formations with tighter splits to take San Francisco out of its press-coverage techniques, the 49ers theorized.

"Receivers know the defensive coaches tell the players not to press if they get tight splits because there is so much room to the sideline," Whitner said. "So our corners had to play off and that is why they did that. It was just a cat-and-mouse game until we figured them out."

The 49ers had trouble getting to their second and third coverage calls in part because they weren't initially sure which routes the Falcons were running from those bunch formations.

"When we make those secondary calls, we are zoning it off," Whitner said, "so you zone it off until a man comes into your area, and then you lock on."

There were some tense moments in the first half as Ryan conducted target practice.

"It gets heated, but we got inside [at halftime] everything was cool," Culliver said. "We talked about what we were going to do when we see those formations. Once you start seeing stuff and start playing the game, you start jumping stuff."

That's what Culliver did when he picked off Ryan at the San Francisco 38-yard line with 7:46 remaining in the third quarter. The 49ers trailed 24-21 at the time and hadn't been able to stop the Falcons to that point in the game.

There was some thought that Falcons receiver Roddy White had slipped on the play, but that wasn't how Culliver saw things.

"Every time Ryan throws the ball, he throws toward the ground where nobody can get it but the receiver," Culliver said. "But I seen it and ran inside on it. A lot of people thought outside, but I ran inside on that and he tried to go down to it, but I got over him and got the pick."

The 49ers' pass rush finally got going late in the game, putting Ryan under duress on six of the quarterback's final 12 drop backs once San Francisco took its first lead 28-24 on Gore's 9-yard run with 8:23 remaining. The 49ers had put Ryan under duress only three times previously on 32 drop backs, according to ESPN Stats & Information.

Despite the late push, the 49ers remained in danger until linebacker NaVorro Bowman blanketed White over the middle and broke up Ryan's fourth-down pass.

"We rose up there at the end," 49ers coach Jim Harbaugh said, "and it was a great finish for our defense -- an exclamation point on the game."

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