The veteran quarterback ran up the sideline back in his own territory, took a hard shot from the linebacker and went down.
He stayed in the game but couldn't finish it and lost his starting job. The career of the player born in Washington State and chosen with the top pick in the NFL draft would never be the same.
No, not Alex Smith.
Try Drew Bledsoe.
On Sunday night, the pros who replaced veteran standouts meet when Brady leads the Patriots against Kaepernick and the 49ers.
By the time Bledsoe, the top pick in 1993, recovered from a sheared blood vessel in his chest in 2001, Brady was entrenched at quarterback. Now, 11 years later, Brady says he didn't feel awkward despite Bledsoe's disappointment at losing his job after being injured.
''It was a long time ago for me, but there was nothing like that on our team,'' he said this week. ''I had great support from all of the quarterbacks, especially Drew, at the time. I don't really know what's going on in San Francisco.''
That's where Smith, the No. 1 draft choice in 2005, suffered a concussion on Nov. 11 in a collision with Jo-Lonn Dunbar of the St. Louis Rams near the left sideline on a 4-yard run to the 49ers 26-yard line.
Smith kept playing, completing his final five passes on the series. He finished it off with a 14-yard scoring throw to Michael Crabtree early in the second quarter.
Kaepernick replaced Smith for the next series and Smith hasn't played a snap since, even though he was medically cleared to play two weeks later at New Orleans.
Bledsoe's injury came in the second game of the 2001 season on an 8-yard run when he was hit in the fourth quarter at the right sideline by Mo Lewis of the New York Jets. He stayed in the game until being replaced by Brady for the final series.
The young backup completed four of five passes to the Jets' 29 but threw incompletions on the final four plays of the Jets' 10-3 win.
So what's it like for the young guy to replace the old guy?
''Am I an old guy or a young guy now?'' Brady said with a smile.
He's 35 now with three NFL championships, two Super Bowl MVP awards and two league MVP awards. When he took over, he was 24 and Bledsoe was 29 with three Pro Bowl appearances.
Kaepernick takes over at age at age 25 for a franchise that had experienced little success over the past decade before Smith took the 49ers to the NFC Championship Game last season in coach Jim Harbaugh’s first year with the team.
Some believe the job is now Kaepernick’s beyond just the present and he’ll be the quarterback of the future for San Francisco as the Niners continue their quest for Super Bowls for years to come with a talented roster and one of the NFL’s elite defenses.
Smith didn’t have quite the track record of Bledsoe when he lost the job to Kaepernick last month, but Smith does stand today as the NFL’s third-ranked quarterback with a passer rating of 104.1 and he continues to lead the league with a 70.0 completion percentage even though he completed his last pass for a touchdown in that Nov. 11 game against the Rams.
''As a player, you just try to focus on what you have to do to help the team win,'' Brady said. ''When you're not playing, you support the guys that are playing. You help out in practice and then when you get your opportunity, you try to go in there and support the team by playing.
''Ultimately it's about winning games. It's not about an individual. It's about doing what's best for the team. So when you play, you've got to play well.''
Kaepernick said this week that he has had nothing but support from Smith since the second-year pro took the starting role from the eighth-year veteran.
“He’s been great,” Kaepernick said. “He’s helped me with everything I’ve asked, even on the sideline he’s going over looks with me, making sure I’m seeing everything.”
Bledsoe was cleared for the 10th game in 2001 and was the No. 2 quarterback but didn't play in it. His next chance came when Brady hurt his left ankle in the second quarter of the AFC championship game.
In his first game in more than four months, Bledsoe threw an 11-yard touchdown pass for a 14-3 halftime lead, then led a field-goal drive and helped take time off the clock with clutch third-down completions. The Patriots beat the Pittsburgh Steelers, 24-17.
''I compare it to giving a starving man a little taste,'' he said then.
But four days before the Super Bowl, coach Bill Belichick announced that Brady would start. And the sixth-round pick delivered, throwing for 145 yards and one touchdown as the Patriots secured the first of their championships with a 20-17 upset of St. Louis.
Now, Harbaugh has chosen Kaepernick over Smith to lead the offense down the stretch. At 9-3-1, a win Sunday would clinch the NFC West title if the Seattle Seahawks lose. The 49ers would still clinch a playoff spot if both win.
''I really don't want to compare it to any other situation, but I think it was a unique situation here,'' Harbaugh said of the quarterback changes. ''Two guys that we believe in, believe can win games for us, and picking one. It's who do you think can give us the best chance for this game?''
Smith and Bledsoe were upset to lose their jobs after being hurt.
''I want to play as bad as I ever wanted anything,'' Bledsoe said at the time. ''I mean, it's the Super Bowl. It's what you play for.''
Smith was even more direct on Nov. 29, the day that Harbaugh announced he would stick with Kaepernick going forward at quarterback even though Smith had recovered completely from his concussion and was ready to play again.
“It sucks,” Smith said then. “I don’t know what else to say. I feel like the only thing I did to lose my job was get a concussion. It’s tough. You kind of state your case with your play, and I felt like I’ve done that.”
When asked if he felt like he’d get another opportunity to reclaim the starting job, Smith replied, “I have no idea. All I can do is just prepare and get ready.”
In 2001, Brady had gone 13-3 in his starts, so he got the call and the Patriots won the championship.
Now Kaepernick is 3-1 as a starter, and he has displayed plenty of promise as a playmaker and potential as a successful performer at the position. Kaepernick has a 97.4 passer rating, is completing 67.4 percent of his passes and he's third among all NFL quarterbacks with 351 yards rushing even though he's only started four games and played sparingly in five others.
And that's what counts, not the feelings of the quarterbacks.
So the considerations in deciding who should play – the recovered veteran or the promising second-year pro – are simple.
''To win. There are no other considerations,'' Belichick said. ''That's the only thing we're really here for is to win. What else is there? I don't know.
''What else is there to talk about?''