49ers GM John Lynch earned his extension, overcoming early draft mistakes and loading up on talent

On the night three years ago after word leaked that John Lynch was expected to be named San Francisco 49ers general manager, a fascinating scene was on display in Houston — in a baseball stadium, of all places.

It was at Minute Maid Park, typically the home of MLB’s Houston Astros, which was the setting for Super Bowl LI’s media night prior to the Atlanta Falcons taking on the New England Patriots. Lynch, then a TV analyst for Fox, was on the network’s stage set up somewhere around where the second basemen usually lines up. About 30 yards away, there was a makeshift podium — really just a seat near the first row of seats by the Astros’ dugout — for his would-be future partner, Kyle Shanahan, who was serving out his final duties as Falcons offensive coordinator.

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The two men’s eyes met for a second that night, as each winked and waved to one another from afar. With scores of media in between, there was no getting closer at that moment.

Both were football lifers, sons of small-college players in the Midwest. They took different paths to NFL success, with Lynch earning his reputation as one of the league’s headiest and hardest-hitting safeties while Shanahan was developing his acumen as one of the brightest-minded offensive coaches in football.

It didn’t hurt that Lynch played for Mike Shanahan, Kyle’s father, for the final four seasons of his playing career.

The partnership of Kyle Shanahan (R) and John Lynch has helped turn the San Francisco 49ers into winners again. (Photo by Michael Reaves/Getty Images)

Lynch and Shanahan were betrothed as something of an arranged (and unconventional) marriage, one that attracted a lot of attention because both were doing their new jobs together for the first time. Through three-plus years together, they’ve proven they’re built to last — and they’ll remain tethered for the future.

After Shanahan received a contract extension earlier this week, Lynch now has his, too.

Shanahan’s extension was viewed as a no-brainer. After the 49ers lost his first nine games as head coach, Shanahan is now viewed as perhaps the league’s most innovative and creative offensive mind. Leading a massive turnaround after only 10 combined wins in his first two seasons, the 49ers landed in Super Bowl LIV and led by 10 in the fourth quarter.

Lynch has been a more interesting and less clear study in the public lens. Despite some early mistakes involving personnel, he — in close harmony with Shanahan and 49ers executive VP of football operations Paraag Marathe — has proven his worth with some savvy moves. It has been an effective, cohesive union to this point.

Especially in the draft, and especially of late.

Overcoming early draft mistakes

The 49ers’ first draft with Lynch and Shanahan aboard was filled with twists and turns.

They started the 2017 draft with the Nos. 2 and 34 overall selections. And they ended the night with Nos. 3, 67 and 31, plus a third-rounder the following year, pulling off two bold trades that got their tenures off to a rousing start.

The fact that the No. 3 pick, Solomon Thomas, hasn’t really panned out or that Reuben Foster, the 31st pick, was cut amid domestic violence charges, didn’t derail Lynch’s reputation or stymie the 49ers’ plans is telling.

It’s what Lynch and the team’s scouting staff has done since that has proven that the team appears to be in good hands for years to come.

George Kittle was the first great draft pick of the San Francisco 49ers' current regime. (Photo by Focus on Sport/Getty Images)

Landing George Kittle in Round 5 that first year was a coup; he might be the best all-around tight end in football. Fifth-round DT D.J. Jones was a sneaky good pick. Third-rounder Ahkello Witherspoon has started several games for the 49ers.

And that 2018 third-rounder they got in the 2-to-3 trade with Chicago? It only resulted in a pick of Fred Warner, one of the best young linebackers in the league. The 49ers also sent their second-round pick that year for Jimmy Garoppolo. Love him or hate him, that was tremendous value and a big feather in Lynch’s cap.

The rest of the 2018 class was similar to the first one: some hits, some misses. Warner is a star and tone setter on defense. First-rounder Mike McGlinchey is a rock at tackle. Fourth-rounder Tarvarius Moore had a big pick in the Super Bowl and could be in line for an expanded role. Seventh-rounder Richie James doesn’t get many chances but makes the most of them.

Dante Pettis could be a whiff from Round 2. Fourth-rounder Kentavius Street has done almost nothing to date. The remainder of the class has made a limited impact.

Lynch’s finest hour: the 2019 NFL draft

But the 2019 class was Lynch’s magnus opus. Starting with Nick Bosa at No. 2 overall, the class was a huge hit after one season. Bosa was Defensive Rookie of the Year. Second-rounder Deebo Samuel has been a multi-tool weapon — perfect for Shanahan’s offense.

The 49ers might not even make the Super Bowl without fifth-rounder Dre Greenlaw’s miracle tackle in Week 17 last year. Sixth-rounder Justin Skule was a terrific eight-game fill-in starter when McGlinchey got hurt. And even fourth-round punter Mitch Wishnowsky performed well.

If Jalen Hurd, the 2019 second-rounder who missed his rookie season with injury, can help replace a banged-up Samuel, this banner group will shine even more.

And lest we forget the undrafted free agents the team has signed since 2017. Matt Breida, Kendrick Bourne, Nick Mullens and Ross Dwelley all have proven to be roster-worthy upgrades. They traded the expendable Breida for a fifth-rounder this offseason but have rebuffed offers for Mullens, who might be in their plans again sometime down the road.

That’s some smart maneuvering. Not bad for a former announcer whose hiring was met with some skepticism, eh? There are several seasoned personnel men serving as GMs who haven’t displayed close to this kind of three-year improvement.

We’ll see how the 2020 class ultimately pans out, but they were once again aggressive in using their limited till of picks to trade up in front of the Green Bay Packers — the team they trashed in the NFC title game — and others to take WR Brandon Aiyuk.

With Aiyuk, first-round defensive tackle Javon Kinlaw (replacing DeForest Buckner) and veteran Trent Williams (acquired with draft assets to replace retired Joe Staley) in the fold, Lynch and the 49ers appeared to make a pretty nifty chicken salad out of what they started with before draft weekend.

Most general managers these days get about three years to prove themselves. And in that time, Lynch has helped turn one of the least-talented rosters into one of the most. They’ve navigated the QB carousel, from Colin Kaepernick’s final days with team to landing Garoppolo, quite deftly. They’ve dealt with injuries by building depth almost everywhere.

Lynch might not yet be regarded in league circles as one of the finest personnel men currently operating. But how can you argue too much against it with his body of work so far?

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