In the midst of a disastrous season, has the 49ers’ championship window closed?

If James Cook can shut down the 49ers defense, Christian McCaffrey can shut down the Bills wing. In that first quarter Sunday night, it seemed only a matter of time before McCaffrey burst past a Bills defender on black-ice and into the end zone.

Instead, he collapsed into a heap in the back yard.

Surrendering.

In the last game – we later found out – he suffered a season-ending knee injury. And that injury could end the 49ers’ season, too. It was the muscle that broke the Camel’s back.

It felt like the 49ers were sacrificing themselves. Not just in the game, which quickly got out of hand, but throughout the season. They now have an 8% chance of making the playoffs, according to Next Gen statistics.

Who knew McCaffrey’s knee could derail the NFL’s national outlook for the 49ers?

Because, now, there is talk of trading coach Kyle Shanahan. There is talk of trading receiver Deebo Samuel, defensive end Javon Hargrave or both. There is talk of reducing the list of aging stars.

What’s wrong with the 49ers this year? Do their problems in 2024 speak of permanent problems? And could those issues close their championship window?

Because it’s one thing for the 49ers to have a fast season. It’s another thing for Shanahan’s run to end.

If you pull up San Francisco’s depth chart before Week 1, you’ll see all the pieces are there: top players at every key position. So let’s go back to that point, shall we? There was not only hope but real confidence.

Quarterback Brock Purdy was the only player with wisps of uncertainty, but he had done enough in 2023 to make the criticism sound like a heated take. Besides, he had McCaffrey, tackles Trent Williams, George Kittle and receivers Brandon Aiyuk and Samuel. Neither quarterback was better — on paper.

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

It would be nice, we measured.

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

And when Mason started struggling, he wasn’t the problem. Aiyuk was playing at an average level. Williams did not pass. That led to the realization that – perhaps – both of them missed training camp (over-holding) with consequences. But having Aiyuk, even playing under his power, was better than not. The 49ers learned the hard way when their WR1 suffered a season-ending ACL/MCL injury in Week 7.

It would be nice, we prepared again.

Aiyuk wasn’t playing that well, and Samuel was on the roster — along with rookie first baseman Ricky Pearsall (who had a shocking recovery from a concussion in late August). Samuel moved into a prominent role, where he struggled under the weight of duties. Kittle remained reliable when healthy, but he also missed a game with a hamstring injury. Without Williams playing at a high level (and then, when he injured his ankle, not playing at all), the 49ers couldn’t produce the same rushing attack.

The pressure was mounting on Purdy.

Making almost as little money as an NFL player would, the quarterback seemed to want to take on more responsibility as his best players went on injured reserve. (Did the upcoming fictitious contract act as a carrot that led him off the cliff?) He was clearly not ready and/or unable to shoulder the burden. His touchdown percentage dropped from 7% to 4%. His yards per attempt dropped from 9.6 to 8.4. His sack percentage increased from 5.9% to 6.3%.

He needed his boys. Maybe not all. But more than that he had.

On defense, the 49ers faced similar problems. Hargrave and safety Talanoa Hufanga were both on IR at the end of September. Defensive end Nick Bosa missed several games. Linebacker Fred Warner was arrested. Cornerback Charvarius Ward, who lost his one-year-old daughter, missed several games due to the loss.

The unit is not what it used to be.

Just as Shanahan has cycled running backs (and, to some extent, quarterbacks), defensive coordinators have done the same thing in the front seven, with a long list of linemen and linebackers. Every year, new actors seem to excel in major roles.

The difference in defense now is that there are signs of confidence in leadership and training. Warner suggested the defense wasn’t fully prepared in Week 12 for what the unit saw against the Packers, surprised them with their running game in the first half. That needs to be fixed, but Warner said the 49ers “have to be better at rebounding.”

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

“I’m very pleased 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 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 reminds us 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 very thin. And that can lead to growing pains.

So back to the original question: What went wrong?

Well, injury, injury, injury. And that probably has to do with age. The 49ers’ roster — back on Sept. 1 — was the third-largest in the NFL.

That leads to the big question: Is their championship window closing?

Injury problems exposed the weakness of the team.

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

That last one could have been killed a lot.

The growth of Shanahan’s coaching tree has made his scheme the most fashionable scheme in the league, leading opponents to build defenses around that scheme. Teams draft and sign players with an eye toward attacking this offense. Mike Shanahan’s coaching tree (including Sean McVay, Matt LaFleur and Mike McDaniel) gave 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 take some big changes. The team can’t just send it back in the hope that it will stay healthy – because the players will be getting old, drinking, and frail. Father Time remains undefeated.

If San Francisco is looking to be optimistic, take the Bills as an example. They are one of the few groups that found a way to renovate the house while they lived in it.

Last season, the Bills parted ways with receivers Stefon Diggs and Gabe Davis, center Mitch Morse, linebacker Tre’Davious White and safeties Jordan Poyer and Micah Hyde. It is true that Buffalo does not miss any of these players. It is also fair to say that the Bills said goodbye at the right time, as those players did not succeed in their respective teams. Meanwhile, Buffalo has seen its young players step up: receiver Khalil Shakir, tight end Gregory Rousseau, linebacker Christian Benford, cornerback Terrell Bernard and safety Taylor Rapp. The Bills have coach Sean McDermott beefing up the defense and Josh Allen beefing up the offensive unit.

But that’s where things get tough for the 49ers. Purdy is not Allen. Not only are they very different players in style, but more importantly, we’ve seen this year that Purdy is not in the conversation in terms of quality. If the 49ers want to rebuild anywhere near as quickly as the Bills (which they did all in one season), they’ll need Shanahan to make Purdy play like he did in 2023. That will require a better offensive line, for starters.

Then they will need a defensive coordinator upgrade. There is an obvious choice: Robert Saleh. The Jets fired him, and while he’s looking for another head coaching job, he won’t be able to find one in the short term. He makes a lot of sense to return to San Francisco for the 2025 season.

The truth is that the 49ers hit the bottom of their winning streak.

They had the best skill players in the NFL and one of the best defenses. But that may be a thing of the past. Their future will be about reloading the depth chart and their coaching positions – while bolstering the elite young core already on the team. And they will have to decide if Purdy is an important part of that future, with the quarterback’s contract expiring in 2025.

There’s a rebuild on the horizon, and it’s easy to imagine that the pace of change and effectiveness will test the job security of Shanahan and GM John Lynch in the coming year. Without an elite quarterback in their midst, the 49ers may not be back in 2025. And that begs the question of whether they will return.

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

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