National Football League

49ers General Manager John Lynch Faces a Dilemma with Colin Kaepernick

Updated Mar. 4, 2020 2:47 p.m. ET

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Fansided, Peter Panacy/FanSided via Niner Noise

John Lynch is now the general manager of the San Francisco 49ers, and one of his first orders of business will be how to handle embattled quarterback Colin Kaepernick.

Congratulations, John Lynch. You’ve just been named general manager of the San Francisco 49ers.

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One of the first things you’ll need to do is figure out the quarterback situation. And that situation includes handling incumbent starter Colin Kaepernick.

It’s going to be a tough choice — one no less polarizing than Kap’s controversial actions from a year ago.

Sure, there are a lot of factors in play here. As we well know, Kaepernick can easily opt out of his contract this offseason and become a free agent. That would solve the riddle. But considering Kap is slated to make $14.5 million in guaranteed money, why would the quarterback want out? he won’t get that money elsewhere.

Plus, it isn’t as if the Niners are laden with other quarterbacking options. The remainder of guys — Blaine Gabbert, Christian Ponder and Thad Lewis — are all free agents. San Francisco needs somebody.

The only question is whether or not Lynch feels Kap is that guy.

John Lynch on Colin Kaepernick

There isn’t much around the web speculating on Lynch’s personal feelings about the quarterback. We certainly know (thank you, Bleacher Report’s Mike Freeman) many NFL executives weren’t thrilled about Kap’s national anthem protest.

Jan 1, 2017; Philadelphia, PA, USA; Fox Sports announcer and former NFL player John Lynch on the sidelines before game between Philadelphia Eagles and Dallas Cowboys at Lincoln Financial Field. Mandatory Credit: Eric Hartline-USA TODAY Sports

Yet many players were supportive of Kaepernick’s actions. Lynch is an executive now, but we can’t rule out his playing days either.

Some of the only material stems from Lynch’s comments on San Francisco’s 95.7 The Game back in 2015:

It’s not an uncommon narrative, but it doesn’t exactly suggest Lynch is a big fan of Kaepernick’s on-field abilities.

The Clean Slate Theory

Another factor — one which likely drew in Lynch and presumed head coach Kyle Shanahan — is the fact San Francisco is embracing a clean slate this offseason.

Aug 11, 2016; Atlanta, GA, USA; Atlanta Falcons offensive coordinator Kyle Shanahan before a game against the Washington Redskins at the Georgia Dome. Mandatory Credit: Brett Davis-USA TODAY Sports

One would assume this includes the quarterback position. Armed with the No. 2 overall pick in the NFL Draft, it’s entirely feasible Lynch and/or Shanahan want to bring in a rookie prospect. This might not push Kap out the door, especially if Shanahan wants to give a rookie QB a year or two to develop. But it’s not a ringing endorsement either.

We also should note Shanahan might have an eye on Washington Redskins quarterback Kirk Cousins, as NFL Network’s Ian Rapoport reported earlier this month:

It’s impossible to determine the level of comfort Lynch has in evaluating quarterbacking talent, especially considering what Shanahan wants.

If this is the case, and Lynch defers to Shanahan, Kaepernick would easily be out the door.

There’s also an interesting parallel between Lynch and his new 49ers gig and that of general manager John Elway joining the Denver Broncos in 2011.

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Remember, Elway had little front-office experience as well when he accepted his position. Yet one of his first orders of business was to move on from then-Broncos quarterback Tim Tebow the following year — a move that certainly iced any relationship between the two.

Will Lynch, in a similar position, feel the same way about Kaepernick?

Regardless, the chances for a Kap return to San Francisco under a new regime remain slim at best.

And it’s possible Lynch’s decision will be an easy one.

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