The 2024 season crashed down on the 49ers like a collapsing wave. A dismal 6-11 record left them buried at the bottom of the NFC West, their first losing season since 2018. The sting was sharper because no Super Bowl runner-up had fallen this hard since 2003. Critics swarmed, questioning coaches, players, and even the front office. But before doubt could take root, owner Jed York slammed the door shut. “You can write that, for sure,” York told. “They’re not going anywhere.” The message was clear—The 49ers tackle front office decisions with unity, says GM Lynch, as they boost their pass rush by adding Bryce Huff to the roster. Kyle Shanahan and John Lynch would stay. The storm raged outside, but inside the organization, the foundation held firm. The fight wasn’t over.

Judging players based on just one season has proven risky; the same also applies to the staff. That mindset may have helped the 49ers find their edge. Finally, the decision was made, and the front office has stayed tight. Everyone seems to back each other fully. “I’ve found the whole discussion on Kyle and some of the stuff rather comical,” John Lynch said. “We have won four of the last five division championships. We’ve been in two Super Bowls.” Both Lynch and Kyle Shanahan signed multi-year extensions in September 2023. Their leadership remains locked in.

In a recent NFL on CBS YouTube video, Lynch repeated how well the team works behind the scenes. He gave fans insight into how challenges are sorted with Kyle Shanahan. After all, nobody expects fairytale-like smooth locker room dynamics throughout the franchise.  He said, “Kyle and I really enjoy each other. We challenge each other, I think. I think that’s something that you have to do.” Even though they do always push each other to achieve their true potential Lynch had passionately defended Shanahan while critics were circling him after a crumbling 2024 season. 

Lynch further adds, “There’s great cohesion. It doesn’t mean you agree on everything but you arrive you have a process where you arrive. Like all right. Here’s where we’re going to go. And I think challenging each other is part of that.” His words seemed aimed at ending talk of tension in the building, which has been circulating in recent years. Shanahan and Lynch started working side by side in 2017, and the duo still “talk about having each other’s back.”

Now, having somebody in the corner is absolutely needed when the star QB is out with an Achilles injury and the defense seems unremarkable. But armed with advice from a tenured Ravens coach, things might be looking up for the 49ers this season.

John Lynch takes advice from John Harbaugh to heart

In the interview, Lynch also shared a story about running into Ravens coach John Harbaugh. The meeting took place at a coffee shop. Harbaugh has led the Ravens for 17 seasons, so when his ‘coach-talks’ hold weight. Over coffee, he gave Lynch advice that showed his years of expertise. Lynch recalled Harbaugh’s words: “Don’t just throw the player out if you can’t agree on them, you know, if you’re passionate about a player. It’s your job to sell Kyle on why that player is a fit for the Niners and vice versa, if Kyle believes in a player, but you’re not quite there. We’ll see if Kyle can get you there because if you’re just throwing them out, you’re missing out on a lot of players, and I thought that was incredible advice and it’s something.”

That advice shaped how Lynch approaches draft talks and roster calls. Trust and communication help the 49ers stay strong. Even when disagreements arise, they seek common ground. The lesson from Harbaugh reflects how the Niners continue to grow despite the departure of several free agents and the addition of 11 new faces to the locker room this season.

Lynch addressed the complete rehauling of the depth chart by saying, “I think it spoke to how good our roster was,” Lynch said. “We had a lot of talent on it and we had acquired a lot of talent, accrued a lot of talent, and people saw that. . . . That’s the hard part, watching good players that are good people, and good people who help build the culture we have here, walk out the door. That’s never fun, but again, it was necessary, and happy where we’re at.”

Lynch acknowledged that the magnitude of the changes is “a tough pill to swallow,” but said the 49ers had to make them. However, that also freed up their cap space, allowing them to sign new talent and extend existing contracts. Quarterback Brock Purdy, tight end George Kittle, and linebacker Fred Warner each signed contract extensions, ensuring the 49ers will keep their core intact as they look to bounce back from a disappointing 2024 season.

Lynch expressed optimism about the team’s draft picks contributing right away, and the team’s track record with talent acquisition and development provides support for that sentiment. However, the actual test won’t come until everything is up and running in September.