Amid a disastrous season, has the 49ers’ championship window closed?

If James Cook could cut through the 49ers defense in the snow, Christian McCaffrey could surely annihilate the Bills’ unit. During that first quarter on Sunday night, it seemed like only a matter of time before McCaffrey would burst past a sliding-on-black-ice Bills defender and coast into the end zone.

Instead, he collapsed in a heap in the backfield. 

Giving himself up. 

On the previous play — we later found out — he’d suffered a knee injury that would likely end his season. And that injury is likely to end the 49ers’ season, too. It was the tendon that broke the Camel’s back.

It felt like the 49ers giving themselves up. Not just in the game, which quickly got out of hand, but also in the season as a whole. They now have just an 8% chance of making the playoffs, per Next Gen Stats.

Who knew McCaffrey’s knee could destabilize the NFL world’s view of the 49ers? 

Because, now, there’s talk of trading coach Kyle Shanahan. There’s talk of trading receiver Deebo Samuel, defensive tackle Javon Hargrave or both. There’s talk of sweeping roster cuts of aging stars.

What went wrong for the 49ers this year? Do their issues in 2024 speak to lasting problems? And could those problems bring their championship window to a close?

Because it’s one thing for the 49ers to have a fluke season. It’s another thing for Shanahan’s run to be over.

If you pulled up San Francisco’s depth chart ahead of Week 1, you’d see all the pieces in place: premium players at every important position. So let’s rewind to that point, shall we? When there wasn’t just hope but genuine confidence.

Quarterback Brock Purdy was the only player with wisps of uncertainty, but he had done enough in 2023 to make criticism feel like a hot take. Besides, he had McCaffrey, tackle Trent Williams, tight end George Kittle and receivers Brandon Aiyuk and Samuel. No quarterback had it better — on paper.

But then came the news of McCaffrey’s Achilles injury: IR.

It would be fine, we rationalized.

Shanahan created a system that has worked best with McCaffrey but has also replaced him seamlessly — so much so that it has made many wonder whether the 49ers needed to give up so much for McCaffrey in a trade in the first place. And for a while, backup running back Jordan Mason put up numbers that were satisfactory. 

And when Mason began to struggle, he wasn’t the problem. Aiyuk was performing at a mediocre level. Williams wasn’t transcendent. That led to the realization that — maybe — the two of them missing all of training camp (over holdouts) had consequences. But having Aiyuk, even playing below his best, was better than not. The 49ers learned that the hard way when their WR1 suffered a season-ending ACL/MCL injury in Week 7.

It would be fine, we rationalized again.

Aiyuk wasn’t even playing that well, and Samuel was on the roster — along with rookie first-rounder Ricky Pearsall (who recovered shockingly quickly from getting shot in late August). Samuel moved into a prominent role, where he struggled under the weight of the duties. Kittle remained reliable when healthy, but even he has missed a game with a hamstring injury. Without Williams playing at a high level (and then, when he suffered an ankle injury, not playing at all), the 49ers couldn’t generate the same game-breaking rushing attack.

The pressure was compounding on Purdy. 

Making almost as little money as an NFL player can make, the quarterback appeared to want to take on more and more responsibility as his best players went to injured reserve. (Did a hypothetical looming contract serve as a golden carrot that led him right off a cliff?) He clearly wasn’t ready and/or capable of carrying the load. His touchdown percentage is down from 7% to 4%. His yards per attempt are down from 9.6 to 8.4. His sack percentage is up from 5.9% to 6.3%.

He needed his guys. Maybe not all of them. But more than he had.

On defense, the 49ers were experiencing similar issues. Hargrave and safety Talanoa Hufanga were both on IR by the end of September. Defensive tackle Nick Bosa has missed multiple games. Linebacker Fred Warner is banged up. Cornerback Charvarius Ward, who lost his 1-year-old daughter, missed multiple games on bereavement.

The unit isn’t what it was.

Just like Shanahan cycled through running backs (and, to some degree, quarterbacks), the defensive coordinators have done something similar in the front seven, with a long lineage of linemen and linebackers. Every year, new players seemed to excel in major roles.

The difference with the defense now is that there are signs of flagging confidence in the leadership and coaching. Warner suggested the defense wasn’t fully prepared in Week 12 for what the unit saw against the Packers, who surprised with their run game in the first half. That required adjustments, but Warner said the 49ers “got to be better from the jump.”

It’s fair to wonder whether San Francisco might fire defensive coordinator Nick Sorensen.

“I’m very satisfied with Nick,” Shanahan said this week. “I’m not at all satisfied with the results and how it’s going right now.”

That statement is not not contradictory.

Sorensen stepped into the role this year after Steve Wilks was fired in February. Wilks followed DeMeco Ryans and Robert Saleh, both of whom went on to become head coaches. It’s reminiscent of what happened to Bill Belichick at the end of his days in New England, when he asked Joe Judge and Matt Patricia to run the team’s offense. They were spread too thin. And that can lead to growing pains.

So to call back to the original question: What went wrong? 

Well, injuries, injuries, injuries. And that’s probably related to age. The 49ers’ roster — back on Sept. 1 — was the third-oldest in the NFL.

That gets to the larger question: Is their championship window closing?

The injury issues have exposed the team’s underlying weaknesses.

1. The offensive line can’t survive without Williams playing like the league’s best offensive lineman.
2. Purdy is currently a good but not great quarterback.
3. Neither Wilks nor Sorensen has maintained the standard of excellence on defense.
4. The 49ers need to replace kicker Jake Moody.
5. And, most arguably, the NFL has caught up to Shanahan’s scheme.

That last one could prove most fatal.

The growth of Shanahan’s coaching tree has made his system the league’s most trendy scheme, which has led to opponents building their defenses around that scheme. Teams are drafting and signing players with an eye to beating this offense. The Mike Shanahan coaching tree (which includes Sean McVay, Matt LaFleur and Mike McDaniel) has given everyone a good look at the offense, and a better chance to stop it.

So the takeaway is that, yes, the 49ers’ championship window is closing as the team is currently constructed. To get San Francisco back to the Super Bowl, it will likely take big changes. The team can’t simply run it back in the hope of staying healthier — because the players will be older, slower, more frail. Father Time remains undefeated.

If San Francisco is looking for optimism, take the Bills as an example. They are one of the few teams that has figured out how to renovate a house while living in it.

Last offseason, the Bills parted ways with receivers Stefon Diggs and Gabe Davis, center Mitch Morse, cornerback Tre’Davious White and safeties Jordan Poyer and Micah Hyde. It’s fair to say Buffalo misses none of those players. It’s also fair to say the Bills said goodbye at the right time, as those players have not excelled with their current teams. Meanwhile, Buffalo has seen its younger players elevate: receiver Khalil Shakir, edge Gregory Rousseau, cornerback Christian Benford, linebacker Terrel Bernard and safety Taylor Rapp. The Bills have coach Sean McDermott maximizing the defensive talents and Josh Allen lifting the offensive unit.

But that’s where things get troubling for the 49ers. Purdy isn’t Allen. Not only are they vastly different players in style, but more important, we’ve seen this year that Purdy isn’t in the conversation in terms of quality. If the 49ers want to rebuild anywhere near as quickly as the Bills have (which they did all in one offseason), they’ll need Shanahan to get Purdy playing like he did in 2023. That would require a better offensive line, for starters.

And then they’ll need an upgrade at defensive coordinator. There’s an obvious option: Robert Saleh. The Jets fired him, and while he probably wants another head coaching job, he isn’t likely to get one in the short term. He makes plenty of sense to return to San Francisco for the 2025 season.

The reality is that the 49ers whiffed on their championship window. 

They had the best skill players in the NFL and one of the best defenses. But that’s likely a thing of the past. Their future will be about reloading on the depth chart and in their coaching ranks — while elevating the elite young core that’s already on the team. And they’ll have to decide whether Purdy is a key part of that future, with the quarterback’s contract set to expire in 2025.

There’s a rebuild on the horizon, and it’s easy to imagine the transition’s speed and efficacy will test Shanahan and GM John Lynch’s job security in the coming year. Without an elite quarterback at the center of it, the 49ers might not be back in 2025. And that begs the question of whether they’ll be back at all.

Prior to joining FOX Sports as an NFL reporter and columnist, Henry McKenna spent seven years covering the Patriots for USA TODAY Sports Media Group and Boston Globe Media. Follow him on Twitter at @henrycmckenna.

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