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If Kaepernick can accept he’s now a backup, Shanahan might keep him

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Editors Note: The previous version of this story used the word cockroach and Colin Kaepernick in the same sentence. The author of the story meant in a way that signals Kaepernick has demonstrated he was able to survive several regime changes in San Francisco. It has since been removed. 

One of America’s most politically disruptive figures is staring a major life decision right in the face this winter.

The marriage between the 49ers and sixth-year quarterback Colin Kaepernick is headed for divorce court in the upcoming months.

The outcomes are pretty cut and and dry for Kap:

A) Opt out of his contract and test a dangerous free agent market. Cities like Buffalo and Miami have spewed negativity on his name in the press and in the parking lots. New York Jets owner Woody Johnson is a Donald Trump supporter. There won’t be a long list of NFL teams begging for his services, and certainly not as a starter.

B) Let the deadline pass in March and risk the 49ers cutting him later, sort of an embarrassing scenario. Kaepernick is technically owed $16.5 million but the 49ers can cut him later and take somewhere between a $2-5 million hit in salary cap.

C) Kaepernick can approach Kyle Shanahan and tell him he’s accepted the fact that he’s now a a 29-year-old backup looking to mentor a young rookie and help out the team in any way possible. He’ll probably have to come to the negotiating table a second time, because $16.5 million is way too much for someone who isn’t playing. Shanahan is probably more comfortable with someone like Brian Hoyer as the backup alongside a promising rookie, but this is Kap’s best chance for staying in the Bay Area.

Jimmy Garoppolo and Kirk Cousins are options, but they seem unrealistic unless the 49ers want to part ways with the No. 2 overall pick. More likely, a rookie comes into San Francisco with a veteran backup possibly bridging the gap. Which means Kaepernick’s realistic best chance for seeing the field in 2017 really might be staying with the 49ers.

Let’s put ourselves in Kaepernick’s shoes for a second. As competitive as he is, he’s become more of a rational thinker in the last calendar year. He’s not naive: the final chapters of his NFL career are about to unfold. Does he really want to uproot his entire life to move to Jacksonville and be the backup for Blake Bortles?

Of course not.

A burgeoning career as a political activist is awaiting No. 7. In the back of Kaepernick’s mind, positioning himself for a life after football is a real thing. Staying in the safe haven of progressive San Francisco is an attractive place for him to keep pushing the envelope with political commentary and protests. Activism is growing by the minute in this country and Kaepernick is one of the few faces who could use his celebrity to win political capital — especially in California.

Here’s the thing about Shanahan: He loves a challenge. He turned a Rex Grossman-Roy Helu-Jabar Gaffney combination into the 15th best offense in the NFL in 2011. Shanahan prefers pocket passers, but he’s worked with improvisational athletes before and done wonders. And we’re talking about the backup position here, not building your franchise around him. Realistically, if Shanahan does have control of the 53-man roster, he might gut this team.

Nevertheless, Kaepernick should want to play for Shanahan, though, and may have to fight verbally to stay on the team. The only quarterback who has struggled with the wizard of a play caller was Robert Griffin III in 2013, who brashly demanded the coordinator change his system to a more traditional offense. Every other QB has produced career best numbers. Playing under Shanahan has been a gift for many careers.

The question will be asked at Shanahan’s first press conference in February: Will you keep Colin Kaepernick?

“We’ll sit down and evaluate every single player on this roster,” you’ll hear Shanahan say. “Colin has done some nice things in this league.”

Nice things are different than consistent things, though. Which is why the smart money is on Shanahan and the new GM doing their best to persuade Kaepernick to opt out — an existing and, at the time, attractive part of his contract re-do in October. Wiping the slate clean at the gunslinger position makes the most sense on paper with this reboot.

Now that we can pick up the broken pieces of glass from a 2-14 season, there were stretches of the year where Kaepernick was the best player on the roster… And other times where he couldn’t complete passes in the second halves of football games. There were highs at Miami and at Arizona… And lows at Chicago and vs. the Jets.

Still, there are so many teams around the league who have worse backup quarterback situations than Kaepernick. The Lions have Dan Orlovsky. The Steelers have Landry Jones. Hell, we even saw the Oakland Raiders fall apart at the seems with Matt McGloin and Connor Cook. Backup quarterback continues to the most undervalued position in the league.

How many of his 16 touchdown passes should be credited to Chip Kelly putting lipstick on a pig — no pun intended. Or how much of it was Kaepernick still having something left in the tank?

That’ll be up for front offices around the league to determine as they assess the pros and cons of adding a player many argued negatively impacted NFL television ratings.

Let’s not forget Kaepernick did win the organization’s prestigious Len Eshmont award, honoring the most courageous and inspirational player. The locker room will have new players and a different vibe next year, but it’s a place where Kaepernick has become a visible leader.

There’s a lot weigh here. And it’s too early to automatically eliminate Kap from the 49ers’ plans in 2017.