Colin Kaepernick's injury timeline indicates a disconnect with the 49ers

Things might get complicated, and potentially ugly, between Colin Kaepernick and the 49ers.

SANTA CLARA, Calif. - Since signing his six-year contract extension in 2014, the San Francisco 49ers haven't done Colin Kaepernick many favors.

After going 8-8 that season, San Francisco parted with Jim Harbaugh, Kaepernick's most staunch supporter who elevated him from promising back up to Super Bowl starter over Alex Smith midway through 2012.

Then, after Kaepernick pledged to take less money to help the team sign key free agents, Frank Gore, Mike Iupati and Michael Crabtree wound up playing elsewhere in 2015. The 49ers fielded the worst offense in the league for most of the season, ranking dead last in both scoring and yardage, on their way to 5-11, before firing Jim Tomsula late Sunday night.

Part of those struggles were a result of Kaepernick's poor play. But the offense was clearly less talented than the units Kaepernick led the three previous years.

Now, his injury status and complications with his contract are becoming sticking points of the offseason as the team looks for a new head coach.

Wednesday, Kaepernick had a pair of surgeries. One on the thumb on his throwing hand and the other on his knee. The recovery from his knee procedure appears shorter than his thumb injury, which he divulged for the first time this week. Additionally, Kaepernick is recovering from shoulder surgery Nov. 24, which landed him on injured reserve in the first place.

It's a very strange and complicated situation, and it might outline a disconnect between the quarterback and front office.

The timeline is notable:

Oct. 4: Kaepernick suffers shoulder injury against the Packers, which does not show up on an injury report until the week he goes on injured reserve.

Oct. 22: Kaepernick sustains a thumb injury against the Seahawks and had his hand wrapped after the game. The injury was reported heading into the next week's game.

Nov. 1: Kaepernick suffers a knee injury against the Rams, gets benched in favor of Blaine Gabbert the following week.

Nov. 21: Kaepernick is placed on injured reserve because of his shoulder injury, a day before the team plays in Seattle with Gabbert as the starting quarterback.

Nov. 24: Kaepernick has surgery to repair a torn labrum in his left shoulder. The timetable for his return was 4-6 months.

Jan. 4: Kaepernick announces his thumb and knee injuries to the media, saying "continued pain" in the thumb led to an MRI last week, which revealed a torn ligament.

Jan. 6: Kaepernick has surgeries to flush loose bodies from his knee and repair a torn ligament in his thumb. The timetable for his thumb is believed to be three months, while he wears a cast for 6-8 weeks, according to the Sacramento Bee. The three-month prognosis would have him recovered the first week of April, after the start of the new league year April 1, which is when he salary for 2016 becomes guaranteed.

Kaepernick never missed a start during his 49ers career before getting benched, which is a credit to his durability and toughness. He played just about all of 2013 with a significant foot injury and didn't reveal it until the next season.

However, Kaepernick waited until well after his recent shoulder surgery to address his thumb and knee, which could have been handled much sooner, giving him a much better prognosis for April 1, giving the 49ers more flexibility in determining his future with the team.

Why Kaepernick waited until this week, and not when he had the shoulder surgery, to have the procedures was a mystery to general manager Trent Baalke.

"I can’t answer that. I think there’s a process that these players go through. That would be a better question answered by our medical staff,” Baalke said.

The key date in all this is April 1, when Kaepernick's $11.9 million salary is fully guaranteed. And without knowing who the head coach will be, how the team handles Kaepernick going forward is very much a conundrum.

"For me, that's not a date I'm concerned with," Kaepernick said. "I feel like I'm going to be playing football regardless of April 1, April 2. I'm doing everything I can to be healthy as soon as I can."

Kaepernick's salary is guaranteed for injury only, meaning if he can't pass a physical April 1 - which is very much in question after having three operations the last two months - the 49ers will be on the hook for his money. To be sure, no team in the NFL wants to pay a back up $11.9 million, if that's how San Francisco views him going forward.

"I’m not worried about April 1 to be honest with you," Baalke said. "I’m more worried about getting him healthy and getting him ready for the offseason program. So, whatever that date is that the medical staff steps up and says, ‘Look, he’s ready to go.’ That’s when he’ll go.”

Baalke should be worried about April 1, because that's the day he could potentially get stuck a monstrous salary cap hit in 2016 for a quarterback who lost his job to Gabbert midway through the season.

Behind closed doors, the 49ers brass can't be thrilled about the timing of Kaepernick's recently disclosed injuries and the fact they weren't handled sooner.

Bottom line: If Kaepernick were healthy in time for April 1, the 49ers could cut him or trade him without having to pay his salary. That was the likely scenario before his recent injuries came to light.

But because he might not be healthy in time, San Francisco might have to pony up even if it doesn't want to, depending on who takes over as head coach.

The timing is all very tricky. And it doesn't appear either side is on the same page.

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SANTA CLARA, Calif. - Since signing his six-year contract extension in 2014, the San Francisco 49ers haven't done Colin Kaepernick many favors.

After going 8-8 that season, San Francisco parted with Jim Harbaugh, Kaepernick's most staunch supporter who elevated him from promising back up to Super Bowl starter over Alex Smith midway through 2012.

Then, after Kaepernick pledged to take less money to help the team sign key free agents, Frank Gore, Mike Iupati and Michael Crabtree wound up playing elsewhere in 2015. The 49ers fielded the worst offense in the league for most of the season, ranking dead last in both scoring and yardage, on their way to 5-11, before firing Jim Tomsula late Sunday night.

Part of those struggles were a result of Kaepernick's poor play. But the offense was clearly less talented than the units Kaepernick led the three previous years.

Now, his injury status and complications with his contract are becoming sticking points of the offseason as the team looks for a new head coach.

Wednesday, Kaepernick had a pair of surgeries. One on the thumb on his throwing hand and the other on his knee. The recovery from his knee procedure appears shorter than his thumb injury, which he divulged for the first time this week. Additionally, Kaepernick is recovering from shoulder surgery Nov. 24, which landed him on injured reserve in the first place.

It's a very strange and complicated situation, and it might outline a disconnect between the quarterback and front office.

The timeline is notable:

Oct. 4: Kaepernick suffers shoulder injury against the Packers, which does not show up on an injury report until the week he goes on injured reserve.

Oct. 22: Kaepernick sustains a thumb injury against the Seahawks and had his hand wrapped after the game. The injury was reported heading into the next week's game.

Nov. 1: Kaepernick suffers a knee injury against the Rams, gets benched in favor of Blaine Gabbert the following week.

Nov. 21: Kaepernick is placed on injured reserve because of his shoulder injury, a day before the team plays in Seattle with Gabbert as the starting quarterback.

Nov. 24: Kaepernick has surgery to repair a torn labrum in his left shoulder. The timetable for his return was 4-6 months.

Jan. 4: Kaepernick announces his thumb and knee injuries to the media, saying \"continued pain\" in the thumb led to an MRI last week, which revealed a torn ligament.

Jan. 6: Kaepernick has surgeries to flush loose bodies from his knee and repair a torn ligament in his thumb. The timetable for his thumb is believed to be three months, while he wears a cast for 6-8 weeks, according to the Sacramento Bee. The three-month prognosis would have him recovered the first week of April, after the start of the new league year April 1, which is when he salary for 2016 becomes guaranteed.

Kaepernick never missed a start during his 49ers career before getting benched, which is a credit to his durability and toughness. He played just about all of 2013 with a significant foot injury and didn't reveal it until the next season.

However, Kaepernick waited until well after his recent shoulder surgery to address his thumb and knee, which could have been handled much sooner, giving him a much better prognosis for April 1, giving the 49ers more flexibility in determining his future with the team.

Why Kaepernick waited until this week, and not when he had the shoulder surgery, to have the procedures was a mystery to general manager Trent Baalke.

\"I can’t answer that. I think there’s a process that these players go through. That would be a better question answered by our medical staff,” Baalke said.

The key date in all this is April 1, when Kaepernick's $11.9 million salary is fully guaranteed. And without knowing who the head coach will be, how the team handles Kaepernick going forward is very much a conundrum.

\"For me, that's not a date I'm concerned with,\" Kaepernick said. \"I feel like I'm going to be playing football regardless of April 1, April 2. I'm doing everything I can to be healthy as soon as I can.\"

Kaepernick's salary is guaranteed for injury only, meaning if he can't pass a physical April 1 - which is very much in question after having three operations the last two months - the 49ers will be on the hook for his money. To be sure, no team in the NFL wants to pay a back up $11.9 million, if that's how San Francisco views him going forward.

\"I’m not worried about April 1 to be honest with you,\" Baalke said. \"I’m more worried about getting him healthy and getting him ready for the offseason program. So, whatever that date is that the medical staff steps up and says, ‘Look, he’s ready to go.’ That’s when he’ll go.”

Baalke should be worried about April 1, because that's the day he could potentially get stuck a monstrous salary cap hit in 2016 for a quarterback who lost his job to Gabbert midway through the season.

Behind closed doors, the 49ers brass can't be thrilled about the timing of Kaepernick's recently disclosed injuries and the fact they weren't handled sooner.

Bottom line: If Kaepernick were healthy in time for April 1, the 49ers could cut him or trade him without having to pay his salary. That was the likely scenario before his recent injuries came to light.

But because he might not be healthy in time, San Francisco might have to pony up even if it doesn't want to, depending on who takes over as head coach.

The timing is all very tricky. And it doesn't appear either side is on the same page.

Follow @ChrisBiderman

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