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He suffered an injury to his non-throwing shoulder last Sunday in the win against Miami that led to him going for X-rays after the game, and then was limited in practice leading up to the season finale.
Would he play Sunday against the Buffalo Bills? If so, how much would he be able to play? And how would this affect the Patriots in the playoffs?
Those questions were lingering Sunday when New England hosted the Bills at Gillette Stadium.
But after the Patriots had overcome a 21-point, first-quarter deficit and demolished Buffalo, 49-21, there were no such questions.
Brady played all but the final series, completing 23 of 35 passes for 338 yards, including three touchdown tosses -- and along the way he became the third quarterback in NFL history to surpass the 5,000-yard mark. Brady finished the season with 5,235 passing yards, second only to the 5,476 yard total rung up this season by the New Orleans Saints' Drew Brees.
He also endured four sacks and a knockdown that drew a penalty as he chased Nick Barnett after the Bills' linebacker had picked off a pass, but emerged seemingly unscathed for the afternoon.
Previously, only Miami's Dan Marino (5,084 in 1984) and Brees (5,069 in 2008) had reached the magic 5,000. Later Sunday, Detroit's Matthew Stafford became the fourth to crash the 5,000 club, with 5,038 yards.
After the win, which secured home-field advantage through the conference finals, there was no talk about the shoulder, just about the 5,000-yard milestone and the Patriots' ability to dig itself out of a huge early hole and emerge victorious.
Brady said he doesn't put much stock in personal numbers.
"I play this game for one reason and it's to win. There's nothing more important to me than that," said Brady, a three-time AFC player of the week this season.
"As a quarterback you do everything you can do to help this team win. When your number is called upon to go out and execute certain plays, that's what you're expected to do. It's not something I think about. It's not something (where I say) 'Man I love throwing touchdowns' or 'I love throwing for yards.' I love winning and that helps me sleep at night," said Brady, who now has thrown 300 touchdowns in his career, tying him with John Elway on the NFL's all-time list.
While this Patriots team didn't have a consistent vertical threat a la Randy Moss in 2007, the abilities of receiver Wes Welker and Deion Branch to work over the middle and occasionally to go deep, plus the immensely talented presences of tight ends Rob Gronkowski and Aaron Hernandez, enabled Brady and offensive coordinator Bill O'Brien to rely on a passing-oriented attack, with the running game mixed in.
"Guys did a lot, catching the ball and running with it," said Brady when asked about going over the 5,000-yard mark. "Our passing game has been obviously a big strong point of this team. The pass catchers and the blockers have been great and we've run the ball great, too, at times. That's what it takes, a complementary offense."
"You run it and we throw it when we need to throw it and we can be effective. You have to stay balanced and those guys have done a great job all year. A lot of it is yards after the catch. (The receivers) are getting open. As a quarterback you just drop back and find them," added Brady, who finished with 39 touchdown passes, making him the first player in NFL history with two seasons of at least 39 scoring strikes, having tossed a record 50 in 2007.
Of course, he was being modest. This team finished 13-3 in large part because Brady was able to put points on the board, and all too often he had to because of a defense that was of the Jekyll-and-Hyde variety.
Sunday was a perfect example. The Pats' defense was scorched for 21 points in the first quarter -- and none thereafter. Similarly last Sunday, New England fell behind early, 17-0, to Miami, but wound up winning, 27-24.
"It's not planned that way," said Brady of the team's penchant for falling behind.
"(But) there's no panic. I don't feel like guys on the sidelines really panic. I just feel like it's really a matter of execution and we started executing better and we put points on the board. It was a fun day to finish 13-3 and win out last eight in a row."
"It's a 60-minute game. We're trying to put it together for 60 minutes. Some days it's been better than others. I like the way we answered today," said Brady. "You never want to get down, 21-0, but if we do, we do, and we have to find a way to battle back."
And with Brady able to shoulder the load, that hasn't been a problem.Steven Krasner is a frequent contributor to ESPNBoston.com.