San Francisco 49ers: Kaepernick Contract Not So Team Friendly After All

Sep 14, 2014; Santa Clara, CA, USA; San Francisco 49ers quarterback Colin Kaepernick (7) looks on during the second quarter of the game against the Chicago Bears at Levi
Sep 14, 2014; Santa Clara, CA, USA; San Francisco 49ers quarterback Colin Kaepernick (7) looks on during the second quarter of the game against the Chicago Bears at Levi /

When the San Francisco 49ers signed quarterback Colin Kaepernick to a big dollar deal following the 2013 season – a contract that’s become an albatross around the neck of the franchise.

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It was an exciting time for the San Francisco 49ers – and for quarterback Colin Kaepernick. They’d just come off a trip to the Super Bowl in 2012 and a very narrow loss to Seattle Seahawks in the 2013 NFC title game. They had a roster full of talented veterans, youngsters on the rise, and a head coach who was pushing all the right buttons at the right time. The world seemed to be theirs for the taking.

And Kapernick, after taking over for an injured Alex Smith and leading them on that improbable Super Bowl run, looked like he was setting the world on fire with 17 wins in his first 23 starts under center. He was a dual threat quarterback who could beat you with his arms and his legs, and many were projecting big, big things for him. With all of the hype and energy, you couldn’t really blame the organization for dropping a pretty penny to keep him locked up.

But oh, how times have changed.

San Francisco, having run off former head coach Jim Harbaugh after an 8-8 season in 2014 – a season of drama and strife fueled in large part by the power struggle between the coach and the front office – crashed and burned, landing at the bottom of the NFL scrap heap.

In 2015, under the “leadership” of head coach – and Trent Baalke/Jed York puppet – Jim Tomsula, the 49ers spiraled out of control and seemed to lose all sense of direction. And the situation within the organization got even worse.

Following the dismissal of Harbaugh and the installation of Tomsula, the team suffered an unusual number of retirements – some expected, some not so much – as well as a number of key free agent defections that left the roster barren and devoid of talent.

The 2015 season had more drama and backstabbing than an average episode of Game of Thrones. The result of the team’s soap opera-esque season was a record of 5-11, the dismissal of Tomusala, and the hiring of another new(ish) head coach in Chip Kelly.

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For Kaepernick, the past two seasons have been an utter nightmare – a nightmare the organization has been forced to live out by virtue of the six year deal worth “up to” $126 million dollars he was given following that close loss to the Seahawks.

With a ton of “guaranteed” money in the contract, it was one that both sides – Kaepernick and the 49ers – could feel good about. It solidified Kaepernick’s status as the face of the franchise and yet, it gave San Francisco plenty of ways to jettison the quarterback and that hefty deal should his play begin to decline.

But after two seasons in which Kaepernick has posted a record of 10-14 – and was benched last season in favor of Blaine Gabbert after going 2-6 in eight starts – he has seemingly lost all the mojo and ability that led the 49ers to give him such a lucrative deal to begin with.

It seems pretty safe to say that his play has declined. And yet, he still remains a 49er.

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After the debacle that was last season, most expected Kaepernick to be jettisoned at the team’s earliest possible convenience – certainly, before the $11.9 million dollar salary he was set to earn became fully guaranteed on April 1.

But that deadline came and went and Kaepernick and his salary remained on the books – despite his request to be traded and the team’s best efforts to do just that.

It was surprising, given that the very team friendly structure of his contract allowed the 49ers to hit the eject button on him. But then word started leaking out that even had the team wanted to get rid of him before the April 1st deadline — which they most certainly did — they couldn’t have because of the injuries Kaepernick sustained last season.

San Francisco 49ers
Nov 1, 2015; St. Louis, MO, USA; San Francisco 49ers quarterback Colin Kaepernick (7) watches play on the sidelines during the second half against the St. Louis Rams at the Edward Jones Dome. The Rams won 27-6. Mandatory Credit: Denny Medley-USA TODAY Sports /

Had they simply cut Kaepernick while still injured, the Collective Bargaining Agreement makes it clear that the team would still be on the hook for his full salary.

So, even though the 49ers thought they’d staged a real coup in signing Kaepernick to a big money deal while still giving themselves a way out of it, because of his injury, their hands were tied and they were stuck with a quarterback who seemed to have lost his magic.

Which brings us to this season. It seems pretty clear that the 49ers are no longer all in on Kaepernick and that Kaepernick wants out of the Bay Area in the worst way possible. It’s a tense situation that – given the front office’s really poor track record when it comes to handling sticky, delicate situations – could cast a pall over the coming season.

The 49ers can ill afford another season filled with drama and backbiting. They most certainly can’t afford the Harbaugh Divorce 2.0.

So what are they going to do? Whether he’s on the roster or not, the 49ers are stuck with his salary for this season. And because of that – as well as Kaepernick’s refusal to take less to help facilitate a trade – San Francisco has been unable to find a trade partner, so they can’t really deal him away.

On the other hand though, they can’t play him either. If they do play him – and he’s as much of a train wreck this year as he was last year – and he happens to get injured again, the 49ers are going to find themselves in the exact same spot they’re in now, next offseason.

And given Kaepernick’s style of play, it doesn’t take a big stretch of the imagination to think that he could very well get hurt again. Especially if he’s forced to play behind a line that saw no significant upgrades this offseason and is virtually the same unit that allowed 53 sacks last year.

The 49ers find themselves in a real jam. Despite Kaepernick’s decline in play, as well as the situation potentially being as big of a distraction as Harbaugh’s final year was, they can’t cut him. They can’t trade him. And they can’t really afford to play him or risk further injury.

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But can they really justify keeping a $12 million dollar backup quarterback on the roster?

It’s a problem without a clear solution. The only thing that does seem clear at this point, is that team friendly deal they signed him to when they thought he was their franchise quarterback doesn’t seem anywhere near so team friendly now.