NFC West: Jed York

SANTA CLARA, Calif. -- San Francisco 49ers CEO Jed York acknowledged in his Monday news conference that it was his decision to let Ray McDonald play to begin the season with the defensive lineman being investigated for domestic violence.

And it was McDonald's behavior that ultimately got McDonald fired earlier this month when he was the subject of a sexual assault investigation.

"When his first issue came up, he was not charged with anything," York said. "We sat down with Ray and said, 'Ray, whether you were guilty or not, you can't put yourself in these types of positions.' And very shortly after that he did that again. You need to make sure people are accountable. That's up to me.

"We might not win the Super Bowl every year, but we can conduct ourselves with class. And we can conduct ourselves in a way that makes me proud. I'll put that on me."

Off-the-field issues, including 10 arrests over a 32-month period, have dogged the Niners in recent years.

"There were other things that we talked to Ray about and there had been incidents with alcohol," York said. "We need to make sure that we are much better with alcohol on this team. And that was one of the things and the next incident that came up with Ray, I have no idea what happened. But I know Ray put himself in another position and it hurts me to know that Ray, who has been a good kid with us, put himself in that position.

"We've had those conversations with Aldon [Smith]. I personally think Aldon's a pretty good kid. He has things that he needs to overcome. When you look back to letting him play in the Indianapolis game (after getting a DUI last year), that was a very, very tough decision and I said that at that point. It's unprecedented that a player would leave in the middle of a season and go to rehab. But, he's got to continue to work on that. He understands that very clearly. And that's something that we need to hold him accountable for and we need to make sure that we keep him going in the right direction."

Smith's name was mentioned in the search warrant affidavit as drinking alchohol with McDonald and the woman who accused McDonald of sexual assault. Smith denied it.

"I talked to the guys today," York said of the 49ers' players. "I talked about winning with class. I said, 'You guys are responsible for how you act outside of this building. Don't get cut because of something you do off the field. You're the one's that control that.'

"And that needs to come directly from me. And when that slips you see level of accountability slip and that's not acceptable. If you want to blast me for something, by all means blast me for that."

Many observers have put the blame for bringing in less-than high quality players at the feet of general manager Trent Baalke. York was asked if he also looks at his GM to draft and sign high quality players.

"Absolutely, absolutely," York said. "And there are guys that, they might not be 100 percent choirboy, perfect quality players, and the NFL is made up of teams that have mixtures of personalities. You need to find a way to get to the guys that are potentially on the edge, that have the ability to really be good guys. And maybe they didn't have the greatest background, they didn't have the greatest upbringing, but that doesn't mean that they're bad people.

"And that's where you get to the teacher (-type coach) to make sure that you find a way to keep those guys instead of going to the other side, keeping them on the side of the road that fits with our core values."
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?

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.

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.

49ers/Harbaugh story won't go away

February, 24, 2014
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.

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
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.

49ers, Harbaugh must come to accord

February, 21, 2014

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
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
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.”
SAN FRANCISCO -- Observed in the locker room after the San Francisco 49ers27-7 loss to the Indianapolis Colts:

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.
Tensions have run a little high on the NFC West blog lately as players and coaches from the various teams have gone back and forth through media.

The reality is that most of the players and coaches involved would treat each other politely in another setting. This was the case during March when San Francisco 49ers coach Jim Harbaugh and his Seattle Seahawks counterpart, Pete Carroll, hung out like old pals during the NFL owners meeting.

It was in this vein that Jed York, the 49ers' CEO and face of ownership, blessed the San Francisco Giants' recent decision to honor Carroll with a personalized jersey.

"Yeah, we obviously compete with the Seahawks and they are going to be very, very tough to beat this year," York told 95.7 FM The Game, "but Pete is a San Francisco guy. He loves the city of San Francisco. The Giants can honor Pete. That is something they are more than rightfully able to do. ... I don't take any offense to that or worry about that at all."

Matt from Berkeley, Calif., used the NFC West mailbag to point me toward the interview, which I had not heard before Monday.

"It's worthy of a blog post about it for the many Niner fans that did not get a chance to hear it," Matt wrote.

The interview was worth a listen, for sure. York covered familiar ground, including the potential for summer practices involving the 49ers and Oakland Raiders. He also reflected on his ownership tenure, noting that he has tried to admit mistakes instead of trying to justify them.

"The first decision I made as president of the 49ers, I hired Mike Singletary," York said. "I thought Mike was the right guy at the time. He turned out not to be the right fit."

The dilemma was clear. "Do I try to preserve my image and try to show that that was the right decision, or do you own up to it?" York said. The 49ers took the latter route, firing Singletary before hiring Harbaugh.

York showed a lighter side throughout the interview, including when hosts Ric Bucher and Chris Townsend alluded to an interview with tight-lipped general manager Trent Baalke.

"I'm sure he said a lot," York deadpanned.

York promised to prepare a Baalke impersonation for a later show, suggesting that Baalke and the Bob Einstein character "Super Dave Osborne" had to be "long, lost cousins" -- the type of reference a CEO makes during a radio program only within the context of a healthy front-office situation.
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?"
Add a $220.3 million naming-rights deal for the San Francisco 49ers' new stadium to the franchise's growing list of significant achievements in recent seasons.

Since 2010, the 49ers have hired a future executive of the year as their general manager, landed Jim Harbaugh as head coach without sacrificing front-office structure, found a franchise quarterback in the second round, drafted an elite pass-rusher in the first round, won two division titles, reached a Super Bowl and secured a new stadium.

Now, add to the list this naming-rights deal with Levi Strauss & Co. -- one of the NFL's richest in total value, according to San Jose Mercury News reporter Mike Rosenberg.

Fans from other teams in the NFC West have probably heard enough about the 49ers' successes. These are nonetheless significant developments for a franchise that had deteriorated considerably from its peak under former owner Eddie DeBartolo Jr. The sun is shining on Jed York, the 49ers' chief operating officer and most visible figure at the ownership level.