Why the 49ers Haven't Extended John Lynch's Contract

Lynch must be feeling kind of weird right now.

When the 49ers extended Kyle Shanahan’s contract, many media people wondered why they didn’t extend general manager John Lynch also. I wondered. Maybe the 49ers will announce an extension for Lynch soon, but you have to wonder.

Lynch must be feeling kind of weird right now. Until the 49ers step up for Lynch, this is how things look to me.

Shanahan did a phenomenal job in 2019. But so did Lynch. Why didn’t the 49ers give him an extension, too? Did he do something wrong? Did he not help build the 49ers into an elite team?

In 2017, the 49ers gave both Lynch and Shanahan six-year contracts. Now, Shanahan is the fifth-highest-paid head coach in the league -- a major raise, while Lynch gets no raise, no raise we know about. And who knows how much more power Shanahan’s new contract gives him? He could become the defacto general manager. Lynch may have just lost power inside the organization. Certainly seems that way.

Shanahan’s father, Mike, always wanted personnel power when he was in the NFL. He wanted to be the vice president of football operations -- the general manager, essentially -- as well as the head coach. And he was the vice president of football operations on the Broncos and Redskins. And he never won a Super Bowl while juggling both jobs. Neither did Mike Holgrem in Seattle.

Does Kyle Shanahan want total control of his team like his dad wanted? Is that what he bargained for?

The 49ers hired Lynch in 2017 precisely because Shanahan wanted to pick the players and Lynch would let him. Lynch doesn’t have a scouting background -- he’s a former player who became a broadcaster. He has no ego when it comes to picking players. He gives Shanahan who he wants.

Trent Baalke wouldn’t do that. Baalke was a former scout with a big ego who got in the way, constantly drafted players his coaches didn’t want. He drafted Tank Carradine in the second round even though defensive coordinator Vic Fangio told Baalke that Carradine didn’t fit the defense. Baalke drafted Carradine anyway and he was a bust. Lynch is so much better than Baalke.

In 2017, the 49ers needed Lynch. They couldn’t make Shanahan the head coach and general manager -- he wasn’t experienced enough. He was 37. Fans and media would have criticized Jed York for giving too much responsibility to a first-time head coach.

So the 49ers hired Lynch, who is respected, polished, sophisticated, articulate and local -- he went to Stanford. He’s a great face of an organization. When the 49ers stunk, he was the deodorant. He covered up their stench. Gave them credibility. Erased Baalke and Jim Tomsula from the memories of 49ers fans. Lynch was important.

But the best deodorant in football, better than a charming GM, is winning. And the 49ers won last season. So they don’t need a figurehead general manager anymore. Meaning they may not need Lynch, and they just told him that by extending Shanahan’s contact and not his, at least for now.

They can give Shanahan total power and no one will criticize them. Everyone believes he’s the superstar of the organization. If they were to fire Shanahan after next season, he would be the top head-coaching candidate on the market, and some team would give him lots and lots of money. The 49ers can’t replace him.

Lynch probably realizes he can bide his time in Santa Clara until his contract expires in 2023, or he can leave and go back to broadcasting, or he can become a general manager somewhere else. He has an excellent resume. He helped build this 49ers team.

If Lynch leaves, the 49ers might elevate his No. 2 guy, Vice President of Player Personnel Martin Mayhew, to general manager. Just a couple weeks ago, Shanahan spoke on a video conference with Bay Area reporters and said the NFL needs more black general managers. Mayhew is black.

Maybe none of this has crossed Lynch’s mind. Or, maybe it has. How else can he interpret the 49ers snubbing him?