Niners quarterback Colin Kaepernick has more than likely played his last down in San Francisco, and the situation surrounding his season-ending injury has left all sides frustrated.
The Niners put Kaepernick on injured reserve Saturday, a surprise move from a timing perspective. The circumstances for the injury ruffled some feathers and accelerated the divorce of the former franchise quarterback and the team he led to the Super Bowl.
Teams almost never learn on a Friday afternoon after a week of practice that they've lost their backup quarterback. That's what happened this week, after Kaepernick practice fully and was listed as probable to backup Blaine Gabbert vs. the Seahawks.
Kaepernick will see respected specialist Dr. Peter Millett in Vail, Colorado, on Tuesday, and the expectation is that he'll have surgery to repair a fully torn labrum in his non-throwing shoulder that day. His recovery can range from four to six months, and which estimate wins out could have monetary consequences.
Kaepernick's $11.9 million in 2016 injury-guaranteed salary becomes fully guaranteed on April 1, and the team has until then to decide whether he's played his last down with the Niners. At least three teams inquired about him at this year's trade deadline, sources said, but no one could take on his salary midseason. San Francisco will explore trade options again this offseason, and it sounds like Kaepernick would welcome a fresh start, as well.
How did it go down? According to several sources, Kaepernick first noticed pain in his left shoulder against Green Bay on Oct. 4, though it's hard to pinpoint when he got injured during the game. It wasn't discussed again for some time.
After he went home for the bye, he came back and reported pain in his left shoulder. The team did an MRI and Kaepernick sought other opinions, as well. On Friday after practice, doctors (including Millett) said surgery was his best option and that another hit to the shoulder would make rehab and a complete recovery difficult.
Kaepernick agreed and informed the Niners of the decision. After assuming they had their backup through the balance of the season, they had to promote Dylan Thompson from the practice squad.
What now?
Kaepernick has no more fully guaranteed money on his six-year, $114-million contract, and he actually lost nearly a million in pergame roster bonuses by going on IR. If he's not on the team next year, it'll hit them with $7M in dead money against the salary cap.
The battle, though, might come around April 1. That's when Kaepernick's contract vests if he's healthy and on the roster. But if he can't pass a physical by then -- which may or may not be the case depending on who does the physical and where he is in his rehab -- the intrigue begins. Does that mean the team is on the hook for his $11.9M salary that is guaranteed for injury? Or if they release him and he plays for someone else (a team would offset the amount the Niners pay on his salary) is that enough to minimize what San Francisco has to pay? If there is a debate regarding the money, it'll likely end up in a grievance.
That said, if Kaepernick is traded, the issue of his 2016 salary would go away because his new team would pay it. That may be the best option for all parties. There is, still, a slim chance he could play for the 49ers next year. But as we know from this year's trade deadline, there is a market for him elsewhere.
Follow Ian Rapoport on Twitter @RapSheet.
