San Francisco 49ers quarterback Colin Kaepernick (7) walks on the sideline during the second half of an NFL football game against the Atlanta Falcons in Santa Clara, Calif., Sunday, Nov. 8, 2015. (Ben Margot/AP)

Kap-ut: QB Done, But Are 49ers Liable?

SEATTLE — Wouldn’t it be flippin’ perfect if they faced each other in a courtroom — the owner who has no clue vs. the quarterback who has no game? Jed York and Colin Kaepernick certainly deserve each other, both having started in the NFL with considerable promise, only to free-fall down parallel dumpster chutes after the foolish firing of the coach who made them look super not long ago.

Jim Harbaugh keeps winning, throwing strip-tease sideline tantrums and proving that he’s one of the best football coaches in the land. And the 49ers keep finding new and astoundingly embarrassing ways to fail as an organization. The latest: York and Kaepernick could be headed toward a legal showdown over millions of dollars, contractual language and the severity of an injury — a torn labrum on his non-throwing shoulder — that officially ended Kaepernick’s season and surely his bizarre 49ers career when he was placed on injured reserve Saturday.

Kaepernicking, it turns out, was a fad, a seed-money app gone bust. The flexed bicep and full-on tats are distant memories now, as are the claims of supposed experts — “I truly believe Colin Kaepernick could be one of the greatest quarterbacks ever,” said Ron Jaworski — that he was revolutionizing the most important position in team sports. Weary of the critical world around him, Kaepernick now can find an escape hatch via his red headphones, and no one will care if he’s on his own island … as long as he doesn’t demand a $11.9-million parting gift from the 49ers, which is possible.

There is no end, apparently, to the relentless succession of turmoil at Dysfunction Junction. Now, the 49ers are looking at another tumultuous offseason that could be dominated by Kaepernick’s recovery from surgery set for this week. Heretofore, York thought he and lead negotiator Paraag Marathe had pulled off the sweetest of team-friendly contracts when they signed Kaepernick to a so-called $126-million extension with a caveat: The 49ers basically could cut their losses, with minimal financial damage, if they traded or released him by April 1 of each year. But the flip side is that Kaepernick’s people wanted protection from injuries.

So if recovery time from labrum surgery takes the usual four to six months, and if other NFL teams are scared off by his health uncertainty, the 49ers will be stuck with an $11.9 million bill in April. They’re the ones who agreed to guarantee most of his $14.3 million salary for 2016 if he’s injured. And they’ll have to eat the money if they can’t find him a landing spot and/or he fails a physical. It was easy to trade Alex Smith, the loser in Kaepernick’s remarkable ascent to the starting job in 2012, when he was healthy and playing well. It will be much harder for general manager Trent Baalke to demand much of anything for Kaepernick, whose poor recent performances and alarming two-year regression are compounded by the labrum tear and last month’s team-motivated leaks that he’s aloof and lacking in leadership.

The big bosses thought they were outsmarting everyone when they benched Kaepernick, gave him an earpiece to hear the play calls and let him roam the sideline with his ever-growing beard. Then he played his trump card: using an injury to his non-throwing shoulder to possibly parlay a handsome settlement. If he initially informed the 49ers’ doctors that the shoulder was bothering him after an Oct. 4 loss to Green Bay — when he was sacked six times and mocked by Clay (“You ain’t Russell Wilson, bro”) Matthews — how interesting that he still managed to start four more games. Obviously, the pain wasn’t so excruciating at that point to keep him from playing, and the 49ers said they didn’t pay close attention to it. Not until the bye week, after he was benched for Blaine Gabbert, did Kaepernick tell the team he was dealing with a major issue the last few days.

Herein lie two suspicious agendas.

By waiting to report his pain as a significant injury until after he had been demoted, is Kaepernick using the injury to quit on his team and not have to be around every day?

And by not having Kaepernick take an MRI until early last week, with the training staff initially telling him that the labrum tear was slight, were the 49ers trying to avoid issues with the $11.9 million payout while concealing news of an injury from the Eagles, Texans, Broncos, Jets and other prospective suitors of Kaepernick?   

Either way, it’s dirty pool.

Not until Kaepernick had a second medical opinion was the injury diagnosed as a complete labrum tear. He’ll have the surgery, and chances are, the Colorado surgeon will say it’s successful. And the 49ers will keep telling us that Gabbert is a roster keeper while they start dropping draft hints about Jared Goff. But some winter afternoon, when the Warriors are 42-1, mark my words that the $11.9 million issue will come up. Kaepernick is bitter enough to demand it. York is bitter enough to battle him because, frankly, Jed’s having trouble beating anyone in anything these days.

Which is exactly why they deserve each other. And why Jim Harbaugh might be the only man on Earth who’s thrilled to have been fired.

Jay Mariotti is sports director and lead sports columnist at the San Francisco Examiner. He can be reached at jmariotti@sfexaminer.com. Read his website at jaymariotti.com.

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