‘It never was about the money really for John’: Why Lynch turned down big money to return as 49ers GM

SANTA CLARA, Calif. — The San Francisco 49ers were less than 24 hours removed from their 2021 season ending in devastating fashion, and coach Kyle Shanahan’s tank was running low.

In the minds of Shanahan, general manager John Lynch and the Niners coaches and players, the season ended a game too early, as they coughed up a fourth-quarter lead to eventual Super Bowl champion Los Angeles Rams in the NFC Championship Game. Now, it was up to Lynch and Shanahan to pick up the pieces before the Niners went their separate ways. Shanahan asked Lynch to address the team with encouraging words for the months ahead.

As a Hall of Fame safety, Lynch had come up short before eventually breaking through by winning Super Bowl XXXVII with the Tampa Bay Buccaneers. With that experience in mind, he wanted to deliver a message centered on the fortitude it takes to push through the pain of losing and come out on the other side better for it.

Everyone listening at the 49ers’ facility knew the faces would change in the offseason, with many players scheduled for free agency and coaches ticketed for other opportunities. Behind the scenes, Lynch was already pondering if he, too, would be on the way out.

In the weeks before the season ended, Lynch had been made aware that Prime Video, which would begin exclusively airing “Thursday Night Football” in 2022, was looking to fill out its broadcasting booth and willing to pay big money for recognizable names.

Lynch, who spent nine years as a color analyst at Fox, was near the top of the list. But as he stood before the assembled players and coaches on locker room clean out day, he couldn’t shake the same feeling of everyone in the room: unfinished business.

“I remember vividly being up there and saying, ‘I can’t leave these guys here,'” Lynch said. “I’m telling them here’s what it’s gonna take … Right then is when I knew.”

What Lynch knew was that regardless of the money, he couldn’t leave because his mission — to bring the 49ers a sixth Lombardi Trophy — was incomplete.

In nearly six years as general manager, Lynch has rarely talked at length about how his time on the job has been. He doesn’t love talking about himself, but recently sat down for a long conversation about the many hats he’s worn as general manager. Yet, he always comes back to the one he wants the most: world champion.

From the moment Shanahan and Lynch arrived in 2017 and reaffirmed with contract extensions in 2020, it’s been their obsession.

“I feel like it’s a demand,” Lynch said of winning a Super Bowl. “It kills me. Like, I can’t even tell you.”

In 2019, the Niners lost Super Bowl LIV to the Kansas City Chiefs. In 2012, before Lynch and Shanahan arrived, they fell to the Baltimore Ravens in Super Bowl XLVII. They again knocked on the door last year, coming up short but holding out hope they’re on the verge of kicking it down.

All of which is why Lynch, even after going through what he calls “the mechanics” of meeting with Prime Video executives and learning what the job might pay — reports indicate it could have roughly tripled Lynch’s salary to somewhere between $12 million and $15 million per year — wasn’t ready to walk away from what he and Shanahan had built.

It’s why Thursday night, when the Niners will try to clinch the NFC West with a victory over the Seattle Seahawks at Lumen Field (8:15 p.m. ET, Prime Video), Lynch will be watching from an owner’s box rather than a broadcast booth. And why Shanahan, who encouraged Lynch to consider the broadcasting job given its massive payday, is happy Lynch is still around to pursue the Lombardi Trophy.

“All I tried to tell him was when you have opportunities like this, like that’s too much to not make the right decision for you and your family,” Shanahan said. “Don’t just do something because you feel loyal to the Niners or loyal to me. It never was about the money really for John … it’s because he really loves being a part of a team.

“We love him here. I think he loves being here and hope he’s here for a long time.”

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IN MANY WAYS, Lynch and Troy Aikman are kindred spirits. Both enjoyed Hall of Fame-playing careers before going on to success in the broadcast booth. What they didn’t know is that each aspired to run an NFL franchise, as they missed being part of a team and going home with a result — good or bad — each Sunday.

Which is why Aikman, who’s the color analyst for “Monday Night Football,” likes to joke with Lynch and Shanahan that had the Fox broadcasting schedule been a little bit different in the 2016 playoffs, Aikman, not Lynch, would be the Niners general manager.

At the time, Aikman worked on Fox’s top broadcasting crew with Joe Buck while Lynch was on the No. 2 team. When the playoff assignments were doled out, Lynch drew the Atlanta Falcons in the divisional round. It was in those production meetings and previous weeks of Lynch covering Falcons games that he and Shanahan, then Atlanta’s offensive coordinator ticketed for the Niners job, began discussing the idea of Lynch coming to San Francisco.

By the time Buck and Aikman were in a production meeting with Shanahan the following week for the NFC Championship Game, they had a good idea Lynch was going to San Francisco with Shanahan, who had been linked to the Niners as head coach for multiple weeks and would take the job as soon as Atlanta’s season ended.

“My first question to Kyle when he came into our production meeting, I asked him, ‘Kyle, are you telling me that if Fox had assigned me the divisional game for Atlanta that I’d be your GM right now?'” Aikman said, laughing. “But John Lynch is an all-time great person. He’s an old-school football guy. A great fit for those two. They’ve had enormous success.”

Lynch’s hiring came with plenty of questions. He would be a first-time general manager who had no formal experience on the personnel side and was joining Shanahan, a first-time head coach.

Shanahan didn’t care about going the unconventional route. He wanted someone who was honest, who could work well with people and would work hard so he could pick up things without direction.

It was an outside-the-box hire for a team that needed a massive rebuild both from a roster and culture standpoint after cycling through three coaches in as many years. At the time, Niners CEO Jed York emphasized the importance of having a tandem that could work through decisions and find the right solution even if they initially disagreed.

Lynch and Shanahan knew each other a bit from Lynch’s four seasons playing for Mike Shanahan with the Denver Broncos. They also shared a common affinity for the 49ers, with Shanahan loving the team as a kid when his dad was offensive coordinator and Lynch playing college ball at nearby Stanford for legendary coach Bill Walsh.

They quickly discovered a shared passion for restoring the franchise to greatness.

“He was the perfect guy to build a team with,” Shanahan said. “Not just the players, but the whole coaching staff, the whole personnel department … You had plenty of guys with experience who could do stuff and he hadn’t had that. But I think most people in that situation, they have a hard time admitting that they don’t know stuff.”

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NEAR THE START of every 49ers practice as players go through stretching and individual drills, Shanahan and Lynch play catch. For Shanahan, it’s an opportunity to loosen his right arm before taking his spot as the quarterback opposite the starting defense during group game plan install.

It’s also a chance for Shanahan and Lynch to stay connected. The pair rarely talk business as they toss the ball around, but their daily routine has roots in a piece of advice Lynch received from former Bucs and Indianapolis Colts coach Tony Dungy when he first took the general manager job.

Lynch, who played for Dungy with the Bucs, remembers Dungy telling him to create opportunities to spend time with Shanahan so necessary discussions can come up organically.

“The general manager kind of impacts the front office and the staff,” Dungy said. “The head coach impacts the coaching staff and the players. And when you get everybody with the same message on board thinking alike, it’s really important. And then in the decision-making process, you want to be together, too. I told John I thought that was really important and I really think he and Kyle have that.”

While Shanahan and Lynch have developed a close bond, Lynch is the eternal optimist that Shanahan jokingly calls “Captain America” while Shanahan is a natural skeptic who prefers to be described as realistic over pessimistic but acknowledges both traits.

When a potential roster move arises, it’s not unusual for Lynch to be met with Shanahan’s immediate cynicism. Shanahan likens the process of big roster moves to buying a house with his wife, where he will point out everything wrong with it to her as a means to determine whether those things can be worked past.

That push and pull, with neither side taking disagreements personally, is necessary. Dungy recalls the Colts’ picking wideout Pierre Garcon in the sixth round of the 2008 draft.

Colts GM Bill Polian viewed Garcon as an intriguing developmental prospect, while Dungy believed the wideout from tiny Mount Union College was too raw. It was the classic battle of long-term versus short-term. The long-term won out and Garcon went on to play 11 years with 628 receptions for 7,854 yards and 38 touchdowns, coincidentally ending his career with the Niners after becoming one of Lynch and Shanahan’s first free agent additions.

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WHEN LYNCH ARRIVED in 2017, he and Shanahan set out on a teardown and a plan to play it conservative on the rebuild. And for the most part, they did. Until October. That’s when they traded for quarterback Jimmy Garoppolo, effectively scuttling their initial plan to try to sign Kirk Cousins in free agency the following March and giving Garoppolo the first shot at becoming their franchise quarterback.

It was the first significant pivot from the Niners’ initial team-building plan and a harbinger of things to come.

After making what Lynch called the easiest decision of his tenure to draft end Nick Bosa with the No. 2 pick in the 2019 draft, then landing receiver Deebo Samuel in the second round, Lynch and Shanahan took stock of what was happening around them. Like the NBA, the NFL was becoming an increasingly star-powered league.

They’ve since made big trades for the likes of left tackle Trent Williams, running back Christian McCaffrey and up the draft board for quarterback Trey Lance.

“It feels like in all of these sports right now, it takes these superstars [to win],” Lynch said. “You understand those guys are essential to winning. The whole team is, every person out there is, but you need those guys. I think we’ve got as many of those guys as anybody. And that’s why we have a chance.”

Those moves have been supplemented by finding some superstars — such as Bosa, Samuel, linebacker Fred Warner and tight end George Kittle — in the draft. And the Niners have found a way to keep most of those players, even when it seemed unlikely. That’s most notably true in the case of Garoppolo.

After a long offseason unsuccessfully spent trying to trade Garoppolo, it seemed there was little chance he would be back. During an August practice, Lynch strolled up to Shanahan and suggested bringing Garoppolo back at a reduced rate. Per custom, Shanahan said “no way,” not because he didn’t want to retain Garoppolo but because he didn’t think the quarterback would go for it.

Lynch preached patience, encouraging Shanahan to let it all play out. Eventually, much to the surprise of many, Garoppolo stayed. Just as Samuel, running back Raheem Mostert and kicker Robbie Gould all had after at one point requesting a trade.

“When [guys like that] come in and say, ‘Hey, I wanna be someplace else,’ you just go, ‘No, you wanna be here,'” Lynch said. “You rely on that good foundation of a relationship you have because you understand those guys are essential to winning.”

That’s not to say, of course, that every move Lynch and Shanahan have made has worked out. Far from it.

Lynch has called trading defensive tackle DeForest Buckner the hardest move he’s made. The trade for end Dee Ford and signing of linebacker Kwon Alexander were big whiffs, and the draft is littered with selections, even near the top, that haven’t worked out.

Even an under-the-radar move like losing cornerback D.J. Reed on waivers still stings. Reed was a fifth-round pick in the 2018 draft whom the Niners believed had starter potential. Heading into his third season, Reed was dealing with a torn pectoral.

After exploring options to keep him, they waived Reed with an injury designation believing he would clear waivers and revert to their injured reserve list. The Seahawks claimed Reed, who became a starter and earned a three-year, $33 million deal from the New York Jets in the offseason.

Lynch acknowledges the misses but doesn’t wince at their mention. He knows mistakes come with the job and likens it to playing safety, where you’re the last line of defense and if you give up a big touchdown everyone knows it’s your fault.

The choice Lynch sees is to dwell on it or learn from it.

“Take note when you really covet a player, don’t try to be cute,” Lynch said. “Those things stick with you but when you’re aligned and you do things together, like everyone’s gotta own it, you know? And I think we all learned from that one.”

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HANGING ABOVE LYNCH’S desk in his office at the 49ers facility is a picture of him and his family from the day he was hired. On a recent afternoon, Lynch looks up at the photo and marvels at how much his family has changed since.

After a one-year delay, Lynch’s family relocated to the Bay Area from San Diego, much to the chagrin of his daughter Lindsay. He jokes that telling your teenage daughter she has to move before her senior year of high school is a bolder move than anything he could do as general manager.

More than anything, he’s sure to credit his family for supporting his decision to leave the broadcast booth.

“I look back, it’s been fun,” Lynch said. “It’s been an adventure. It’s been worthwhile. It’s been fulfilling, I’m very appreciative of my family, very appreciative for the opportunity.”

One of the first things Lynch said after taking the job was that he didn’t know what he didn’t know. In order to learn, he took another cue from Dungy and surrounded himself with people he believed in.

Paraag Marathe, the Niners’ executive vice president of football operations, and Brian Hampton, the team’s vice president of football operations, have been instrumental in handling salary cap and contract issues, an area Lynch says is a work in progress for him.

Assistant general manager Adam Peters is his top lieutenant and player personnel director Ran Carthon has been key in assisting with scouting talent.

Both have interviewed for general manager jobs elsewhere in the past year. Either would be a candidate to replace Lynch if he left.

“We have a lot of people on the staff that we’re always trying to groom,” Shanahan said. “Not just to replace one of us someday but also to help them get opportunities in other places. We’ve got lots of good guys here that we feel confident in but John’s our guy and I hope that we don’t have to deal with that for a long time.”

By his own admission, Lynch is almost too focused on the here and now, rarely looking beyond the 24 hours in front of him. Which means he’s spent little time considering when he might be done in San Francisco’s front office.

Lynch works in a building with constant reminders of the Niners’ five world championships. He admits he doesn’t see himself walking away until he’s added at least No. 6.

“I’m still very motivated to get up and come to work every day,” Lynch said. “I’m challenged and I’m enjoying myself. I’m still motivated to get this place back to where it once was. And that’s on the top.”

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