Colin Kaepernick was already under contract with the San Francisco 49ers when he was named the team's starting quarterback Tuesday. That goes without saying.

Kaepernick had gotten what he wanted -- his starting job back -- and was, according to 49ers coach Chip Kelly, under no obligation to sign a new deal.

He signed one anyway.

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The reasons why he did are complicated and disjointed: The 49ers surely didn't want to play Kaepernick if his injury guarantees were still on the books, but Kelly said that the front-office had no bearing on his decision to name Kaepernick the starter.

Someone in that situation is lying. Considering how the situation ended, it's hard to believe one side.

But here's the real question: Why did Kaepernick sign a new deal, eliminating the last four years and nearly $80 million in earning potential of the contract he signed in 2014?

The answer: He didn't have much of a choice, and his National Anthem protests were a big reason why.

Kaepernick was benched last year for Blaine Gabbert, and he was likely to be cut before the 2016 season started. He avoided that fate by invoking the injury language in his contract, which didn't allow the 49ers to cut him while he was in the process of rehabilitation, as he was throughout this past offseason.

In turn, Kaepernick was guaranteed nearly $12 million on April 1, 2016 -- the bulk of his annual salary.

Given the 49ers' incredible salary cap room, the team was content with having their backup quarterback be one of their highest paid players.

But Gabbert has been so poor this year that Kelly turned to Kaepernick to right the ship -- though we don't know if he had any contact with the 49ers' front office about that.

What is clear is that the 49ers front office had little interest in playing Kaepernick so long as that injury language was still in his contract -- they didn't want to risk him getting injured in a game, only for him to invoke the contract language again next offseason. If Kaepernick was still on the roster, either through team choice or because he was rehabilitating from off-season injuries, on April 1, 2017, he'd be owed more than $14.5 million. The 49ers couldn't risk that.

Whether Kelly wants to admit it or not, it's evident that the 49ers were willing to go to third-string quarterback Christian Ponder if Kaepernick's contract was not amended to alleviate the team's concerns over the injury clauses. If Kaepernick had not renegotiated, the quarterback would have assuredly been cut at the end of the year, making him a free agent.

The 49ers clearly explained that scenario to Kaepernick -- you can get cut at the end of the year without having played, or you can restructure your deal so that the injury language is gone and then play out the remainder of 2016 as the starting quarterback.

Kaepernick had to choose the latter option -- no one is going to sign a quarterback who was last seen being benched for Gabbert, particularly if he's the center of a media firestorm regarding his protest during the National Anthem.

The truth is that Kaepernick wasn't good enough to have teams look the other way at the "distraction" they'd surely deem (or have deemed) his anthem protest.

And while the anthem protest isn't going away now that Kaepernick is the starting quarterback for the 49ers again, it's negative effects on Kaepernick's possible free agency (don't be naive, no matter where you stand on Kaepernick's protest, NFL teams were not going to expose themselves to that level of outside scrutiny) can't be glossed over. The anthem protests could have easily derailed Kaepernick's' career.

The worst thing you can be in the NFL is "not worth the trouble". That was going to be Kaepernick's fate, fair or not.

Kaepernick has already been paid the bulk of his salary this year -- given everything that's happening around him, the other 31 NFL teams are going to need a damn good reason to sign him. What's the harm in restructuring if the 49ers have made it clear they plan to cut you at the end of the season anyway?

Kaepernick had a dead-end deal with the 49ers. His new deal -- no matter how much the NFLPA might hate it and no matter how many eyebrows it raised around the sport -- gives him a chance to prove that he's worth the "trouble" after all.