Alex Smith has been supplanted as starting quarterback of the 49ers by Colin Kaepernick. Though Jim Harbaugh still has to carefully go through the motions of weighing the decision of who to start each week so as to be diplomatic about the change, it’s clear that it’s Kaepernick’s job. It was evident before halftime of the Monday night win over the Bears two weeks ago. A capable quarterback that fans of the team have been waiting on even before Harbaugh was even coach had arrived and the long-term project that was transforming Alex Smith from total shitheap into a passable game manager had come to an end.

People are already writing long thinkpieces musing on the similarities between this situation and what the 2001 Patriots went through with Drew Bledsoe and Tom Brady. I think it might be juuuuuusstt a bit premature to liken Kaepernick’s career with that of Dreamboat, but the dynamic holds up. An injury knocked out an established but uninspiring starter. A not much heralded backup gets an opportunity because of injury. It’s evident right away that the backup is better. It’s not just a circumstance like Tebow that the team is winning with him. He’s better. Alex Smith is done the same way Bledsoe was. Even if Kaepernick gets hurt for a bit and Smith has to make a reappearance. Recall that Bledsoe had to come back to save the 2001 AFC Championship because Brady got hurt against the Steelers. That still couldn’t save the job for Bledsoe.

Come the off-season it’s time for Alex Smith to move on. He should have known this time was coming. Apparently, knowing it was coming didn’t make it any easier, according to teammate Joe Staley:

“He wants to play. He made his feelings known yesterday with the comments that he made. He’s itching to play, and he feels he should be out there, but it’s the coach’s decision. That’s the way he’s handling it. … I know it’s eating him up inside, but I know Alex, the kind of man he is, the kind of character he has, and he wants to see the team win. But he wants to be out there on the field.”

Sorry, can’t feel bad for Alex Smith. It’s not even the years of being considered a bust as a former no.1 overall pick. It’s that he walked into this. The 49ers gave him every indication after last season, even with nearly making it to the Super Bowl, that they would rather have just about anybody else under center for them in 2012. They opened flirted with Peyton Manning in free agency. They wouldn’t give Alex Smith a modest contract extension. They let him explore his options in free agency. Alex Smith met with the Dolphins, a mediocre team that would have been perfectly happy to have him. Rather than sign somewhere that his job would be more secure but his supporting cast wouldn’t be as good, he came back to the 49ers with his tail between his legs. He basically signed out for this very scenario to play out at a later date.