Chip Kelly announced the move Tuesday.
This puts an otherwise innocuous matchup against Buffalo firmly in the spotlight for multiple reasons.
1. The finances
Kaepernick was one of the reasons many people believed Kelly was attracted to the 49ers job, but injury issues and contractual obligations have kept him from seeing the field.
Many believed the 49ers would not risk playing Kaepernick until a new contract extension was reached (Kap basically was stuck on the roster because he wasn't able to pass a physical, which in turn guaranteed his salary for 2016 -- the team is worried about him getting injured and guaranteeing it for next year as well).
According to CBS Sports NFL Insider Jason La Canfora, the two sides haven't officially brokered a new deal yet.
Chip Kelly announces Colin Kaepernick is his starting QB. As of now, no paperwork on a revamped contract filed yet— Jason La Canfora (@JasonLaCanfora) October 11, 2016
It's possible that new deal is hammered out before the week begins, or maybe the two sides have a gentleman's agreement on Kap's deal. Basically the 49ers don't want to be on the hook for his fully guaranteed salary next season should he suffer an injury.
2. The football
Last we saw him playing actual football, Kaepernick wasn't very good. In fact, he was bad. He got benched for Gabbert! But the 49ers look like a team lost in the limbo of bad roster decisions and they need to try and make some sort of change in order to kickstart the offense, which has looked highly lethargic under Gabbert for much of the season.
Kaepernick was a disaster when last we left him, but has at least had success on an NFL field. The same cannot be said for Gabbert.— Patrick Daugherty (@RotoPat) October 11, 2016
Kaepernick starting. Wouldn't have high expectations but he's a huge improvement over Blaine.— Cian Fahey (@Cianaf) October 11, 2016
Even if Kap doesn't have the accuracy and passing skills to succeed as a traditional passer, he does have piles of athleticism to potentially exploit defenses in Kelly's system.
Kelly himself needs a little juice. Kaepernick might provide it. Or he might not. It ultimately isn't going to make the 49ers good, but it might make them better.
3. The anthem
Without playing a single down of regular-season football, Kaepernick has become the most talked-about player in the entire NFL this season.
His decision to sit and then kneel before football games in protest of the national anthem has created controversy around the NFL and in the general world.
A Supreme Court justice weighed in on the issue Monday, calling the protest "really dumb." People are still talking about his actions, even if the weekly chatter has died down since the season began.
It should ramp back up on Sunday with Kaepernick starting. His move to the role of starter means even more focus and it means even more attention before the game begins. The 49ers-Bills game that no one was going to watch is suddenly must-see television, for what Kap will do before, during and after.