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General managers need bye weeks, too.
Especially if you’re a 49ers executive who lived through the 6-11 collapse in 2024, sorted through a major financial and depth-chart reset in the offseason, then helped Kyle Shanahan deal with so many punishing injuries in the first months of the 2025 campaign.
Yes, you can tell: The 49ers’ players absolutely craved the much-later-than-usual break last week to soothe their bruises and wounds after getting through the first 13 weeks in a row at 9-4, but John Lynch sure was invigorated by it, too.
And now Lynch, the Hall of Fame former power-hitting safety, can’t wait for Sunday’s game against the Titans and the start of the last lap of this fascinating season.
“This time of year, people always ask me, ‘Do you miss playing? Do you miss it?’” Lynch said on my podcast Monday. “And usually early in the season, I don’t at all. I played 15 years. I left it all out there and I left on my own terms, so I’m pretty good with it. But around this time, and certainly come playoffs, I still wish, even at 54, years old, I could get out there.
“So it’s a good time of year, and I like where our team’s at.”
The 49ers, as Lynch notes, are in very solid position for an NFC playoff spot — either as a dangerous wild-card team or, if they go 3-1 or 4-0 to the regular-season finish line, the NFC West champion and an outside shot at the conference’s No. 1 seed.
In the bigger picture, the 49ers are in even better shape — Shanahan, Lynch, and owner Jed York committed to a major overhaul last season that, in Shanahan’s words, ideally opened up a new three-year window of contention.
Left unsaid but not that unsaid: The 49ers didn’t quite expect to contend for the top of the conference in Year 1 of the recalibration. They knew they still had great players, but especially when they lost two of their best — Nick Bosa in Week 3 then Fred Warner in Week 6 — for the season, the 49ers’ brass figured they were mostly setting up for the biggest returns in 2026 and 2027.
Throw in Brock Purdy missing eight of the first 10 games after signing a new, $265-million deal, and injuries to George Kittle, Ricky Pearsall, and Mykel Williams… and who could’ve expected that the 49ers would get to the bye week with a puncher’s shot in a wide-open NFC race?
They’ve done their reset. They’ve gotten younger. They’ve gotten cheaper. They’ve won some close games. They’ve been scrappy. They’ve over-achieved. They’ve got vulnerabilities, but they’re covering them up increasingly well. They’ve got Purdy, Kittle, and Pearsall back. They’ve had Christian McCaffrey and Trent Williams powering through all season.
Kyle Shanahan, left, and Lynch have worked together since 2017. | Source: Thearon W. Henderson/Getty Images
I didn’t think they were going to be this tough and this successful this swiftly in the new cycle. I don’t think they did, either.
So this winter sets up as kind of a free roll for the 49ers, who aren’t the favorites but sure could mess up a few higher-regarded teams in the playoffs.
But first, Lynch and Shanahan had to get through the offseason discardings of Deebo Samuel, Dre Greenlaw, Talanoa Hufanga, Javon Hargrave, Jordan Mason, Charvarius Ward, and many others.
3 days ago
6 days ago
Tuesday, Nov. 25
“You wish you could sign them all,” Lynch said. “What I would say to that is, our ownership has been tremendous since Kyle and I have been here. They’ve let us be extremely aggressive and have been incredibly supportive of, if we think it’s going to help us win, all right, we’ll make it happen. Now, when you do that and you’re one of the top cash-spend teams, there’s always going to be a cap consequence …
“I’d say last year we kind of went for it because we felt like we had such a good roster that it’d be a shame not to. … And it didn’t work out.”
The payroll had to get thinned down after multiple all-in seasons. And Lynch and Shanahan had another focus.
“Probably more important, we didn’t want to become an aging roster,” Lynch said. “We had to find a way. We also knew we had to pay our quarterback. We had made a decision organizationally that we felt that was the right thing to do.”
Shanahan and Lynch relied on the younger players on the roster to move into more prominent positions. They relied on hitting most of their draft picks this year. They relied on the culture of the locker room to hold things together.
Then the injury wave crashed into them, similar to the emergencies of 2024, and this time the 49ers didn’t crumble. They’ve pulled out some tight victories. They’ve built confidence. They fixed the special teams. They’ve taken advantage of a weak schedule. They’re gunning for a good playoff seeding, and who knows what happens after that.
Pretty good for a free roll.
“I’m proud that we navigated it the way we did,” Lynch said. “We had a core group of players that we felt, if we could thoughtfully mix some youth with it could be a great combination. Having said that, not real easy to do. That was tough on Kyle and I, But it was tough on everyone. And, you know, we did it, and I think we’re better for it.”
Are you ahead of schedule, maybe, John?
“I don’t know about that, because I think the story’s not written yet,” Lynch said. “We’ve given ourselves an opportunity.”
There’s another opportunity beyond this season: Given their salary cuts last offseason and more recently the voiding of more than $24 million in money that was initially guaranteed to Brandon Aiyuk in 2026, will the 49ers spend more in the next free-agent cycle?
“We’ll see whatever the situation is,” Lynch said. “I think it’s really important that you spend it wisely. (Going heavy on the draft), man, that’s a fun way to build it, and it’s probably the way that you should focus on now; we’ve had success through the draft. …
“I’ll tell you, it’s healthy for your team to keep adding and infusing youth. It’s a young man’s game, and I just like the combo (of youth and experience). So whatever we have, we’ve got to just be committed to spending it wisely. Because we’ve rewarded a lot of players around here, and there are consequences for that. But I think so long as you manage it well, we can keep this thing going.
“And hopefully that’s what some of our actions from last year will set us up for years to come, that we can keep this thing sustainable.”
Trent Williams has been a cornerstone for the 49ers at left tackle since Lynch and Shanahan acquired him in 2020. | Source: Brooke Sutton/Getty Images
Here are some more highlights from our conversation …
• When I asked Lynch if he’s disappointed that Aiyuk’s relationship with the team has fractured so quickly after the two sides agreed on four-year, $120-million extension in August 2024, Lynch emphasized that Aiyuk’s devastating knee injury last season affected a lot of things.
It also, of course, led to Aiyuk reportedly missing or being late to rehabilitation sessions at 49ers HQ over the spring and summer and the 49ers in July canceling the guarantees — and presaging the end of Aiyuk’s time with the team.
“I think watching a player go through that is tough,” Lynch said. “Some of the other things that’ve happen on the side, you know, haven’t been fun, but (sometimes) you go through that with players. Like I’ve talked about throughout this thing, that story’s not written yet. And Brandon’s still working to try to come back from his injury, and hopefully, his story is not done with the Niners, and there’s still a great ending to it.”
This is me, not Lynch: But Aiyuk still hasn’t started practicing, with only four games to go, and it seems most likely that he has played his last game with the 49ers and will be traded or released in March.
“When you make a commitment to a player like that, you know your hopes are everything goes smooth and all that,” Lynch said. “That’s not always the case.”
• Lynch suggested that the 49ers signed veteran QB Mac Jones to a two-year deal last offseason, not a one-year deal like Sam Darnold two seasons ago, because they learned a bit from helping to resuscitate Darnold’s career then losing him immediately in free agency.
Could that mean the 49ers have set this up to trade Jones in the offseason after he won five games subbing for Purdy and showed that he probably should be a starter somewhere in 2026?
“You know, ‘could’ … we could always do something,” Lynch said. “But this position — nobody exhibited this more than the great Bill Walsh (by stockpiling Steve Young behind Joe Montana). The more quality players you have in that (QB) room, that sets you up for success. (But) I think you’ve got to keep your eyes and ears open to everything.”
• Lynch is understandably pleased with the contributions of defensive lineman Keion White since his acquisition just before the trade deadline.
Were the 49ers close to landing anybody else — maybe Jaelan Phillips, who ended up going to the Eagles for a third-round pick?
“We were in on some of the big names,” Lynch said. “I think it was kind of a seller’s market. … There were a lot of teams looking and so the asking prices were just crazy, and we weren’t going to do that.”
• As Lynch and Shanahan come to the stretch run of their ninth season together running this team, I asked if Lynch has any general conclusions about what got the duo here and how long they might continue doing this.
“I came here to get something done, and that was kind of to help a really proud organization get back on track and win championships — compete and win championships,” Lynch said. “We’ve done the compete part. We haven’t won it. And when I get my mind set on something, I really want to see it come to fruition. And I’m having a really good time doing this right now.
“I will tell you the conclusion I have is I never thought I’d be here this long. … I don’t think I thought it’d be easier, but I probably thought we’d have a couple in our in our hip pocket by now; and that hasn’t happened.
“We’ve had good chances, but we haven’t paid them off. And so I’m committed to trying to pay this thing off having a good time. I feel excited about where our organization is at. And I think the arrow is pointing up.”