
Welcome to “NFL Thoughts,” a wide-ranging, in-depth look at some of the top storylines of the 2025 season. We started this year’s series by looking back at the prized 2024 rookie quarterback class and looking forward to what we should expect from it in 2025. Today, we’re looking at a team that fell off in 2024 and whether it can rejoin the NFL’s upper crust after big changes over the 2025 offseason.
From 2019-2023, the 49ers won 54 regular-season games — only the Packers won more games among NFC teams — and went to two Super Bowls, falling to the Chiefs both times. The 49ers’ eight playoff wins over that span were second in the NFL, only behind Kansas City. That Patrick Mahomes guy has a way of standing in the way, doesn’t he?
In last year’s version of this very series, we wondered aloud if 2024 would be the 49ers’ last run as we knew them. They were dealing with contract drama and injuries, but they were still, on paper, one of the NFL’s more talented rosters. They had just come one possession away from lifting the Lombardi Trophy, Brock Purdy blossoming with tons of stars around him, and the defense returned several standouts. San Francisco had, by cash spending, the most expensive roster in the NFL.
Then things fell apart. Injury concerns became an injury epidemic — the 49ers were by far the team most impacted by injury per Aaron Schatz’s adjusted games loss metrics — and new, unexpected issues piled up. The 49ers went 6-11, their worst record since 2018.
Can they get back to their standard? The NFC West has the team that came closest to beating the Eagles in the playoffs — the Rams — as well as a 10-win Seahawks team and a Cardinals club with a remade defense. It won’t be easy — things in the NFL rarely are — but San Francisco hopes a seismic offseason plus significant internal improvements get the team back on track.
49ers offense: Is improved health enough?
Things began poorly for the 49ers and only got worse. Christian McCaffrey’s mysterious nagging Achilles went from offseason worry to preseason worry to early-season worry to causing him to miss the first eight games of the season. Then he suffered a knee injury in Week 13 and missed the rest of the season.
Brandon Aiyuk’s contractual standoff led to a slow start to the season. In Week 7, he tore his ACL. Trent Williams‘ contractual standoff also got resolved, but he hurt his ankle in Week 11 and didn’t play again.
In 2023, McCaffrey and Aiyuk combined for 3,365 yards from scrimmage and 28 touchdowns. In 2024, they combined for 722 yards from scrimmage and zero touchdowns.
It’s easy to say things will be fine with that triumvirate back in action — but it’s also foolhardy.
McCaffrey’s Achilles issues came one year after a Herculean 2023 in which he led the NFL in touches, yards from scrimmage and touchdowns scored. McCaffrey has led the NFL in those three categories twice, the other coming in 2019. He missed most of each of the next two seasons. We’re halfway there this time around, and now he’s 29 years old.
McCaffrey is indispensable for this team, and it shows up most in the passing game.
Rec/Rec yds/Rec TD |
67/564/7 |
29/267/0 |
YAC per rec |
6.9 |
6.3 |
First downs or TD rec |
31 |
14 |
McCaffrey had more catches for first downs/touchdowns in 2023 than the non-McCaffrey running backs had catches, period, in 2024. This really hurt on short throws — both designed and checkdowns. In 2023, the 49ers led the NFL in expected points added per play on throws to running backs 5 yards or fewer downfield. In 2024, they were 17th.
Don’t forget about the running game, either. San Francisco was third in expected points added per rush in 2023. It was 17th in 2024.
Predicting health is fool’s errand, but there’s no denying McCaffrey adds a completely different dimension to the 49ers’ passing game, one that didn’t exist last year.
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The rest of the weapons are up in the air, too. Aiyuk isn’t expected back for the start of training camp. Ricky Pearsall got shot in the chest before last season began and miraculously not only survived but came back to play by Week 7. He emerged late in the season, including an 8/141/1 Week 17 against the Seahawks, but suffered a hamstring injury in OTAs. Both he and Jauan Jennings, the hard-nosed blocker who showed real chops as a receiver last year, have important years ahead.
What the 49ers don’t have is Deebo Samuel, whom they traded to Washington after a disappointing 2024. Even in a down year, Samuel led all receiver in average yards after the catch (8.3), and his skill set can’t be duplicated. Perhaps we’ll see a more downfield-based approach when it comes to targeting wide receivers this season, with McCaffrey eating up work underneath.
The overlooked aspect of the 49ers’ offensive downfall in 2024 was the line play. There are major questions in 2025. Colton McKivitz has been inconsistent at right tackle, and Williams, who turns 37 next week, posted his lowest Pro Football Focus grades since he arrived in San Francisco in 2020.
At right guard, 2024 third-round pick Dominick Puni appears to be a gem, but there are questions at left guard. A potential battle between Ben Bartch, who had started 10 games in the last three years, and Spencer Burford isn’t promising. Center Jake Brendel has graded out as a solid run blocker but poor pass blocker each of the last two seasons.
And then there’s Purdy, the most relevant Mr. Irrelevant ever. Purdy was never going to match his all-time efficient 2023, but without McCaffrey to lean on, he struggled in several aspects, especially when pressing the ball downfield.
Comp pct |
55.3% |
40.8% |
TD-Int |
7-0 |
2-2 |
Off-target rate |
12.8% |
22.4% |
EPA per dropback |
1.17 |
0.54 |
Purdy is always going to be a bit of a gambler. It’s how he plays the position, which leads to higher highs than previous iterations of Kyle Shanahan’s quarterbacks but also leads to some truly head-scratching lows. On the other hand, Purdy’s not fully to blame here. The 49ers as a team ranked last in average target separation per NFL Pro. Using ESPN’s Receiver Scores, Aiyuk went from having the eighth-best “open” score among wide receivers and tight end in 2023 to 77th in 2024. Samuel was 102nd.
The hope is that McCaffrey provides more outlets underneath and Pearsall and Aiyuk (eventually) can join the superb George Kittle in creating openings downfield.
One final thing on Purdy: He scrambled on over 8% of his dropbacks last season, more than double his 2023 rate, and he was actually quite proficient at it. During Shanahan’s time with the 49ers, his play action usage has gradually declined. In 2019, San Francisco used play action on nearly one-third of its dropbacks, the fourth-highest rate in the league. Last year, it ranked 22nd.
Purdy, however, has been an effective under-center, play action team in his career. Without a quick-strike YAC weapon like Samuel and with McCaffrey’s return hopefully providing a boost to the rushing attack, more play action could be in the cards, with Purdy’s mobility becoming a bigger part of the passing attack.
49ers defense: How quickly can newcomers contribute?
The 49ers’ issues running the ball were startling but not shocking given the injuries.
Their issues defending the run were absolutely shocking.
Success rate |
52.1% |
On Record (since 2000) |
Expected points added per rush |
-0.02 |
2000 |
Missed tackles |
87 |
On Record (since 2017) |
Yards per rush before contact |
1.63 |
2019 |
Run stuff rate (0 yds or fewer) |
19.5% |
2019 |
It was bad all the way around. The 49ers had seven defensive linemen/EDGEs/linebackers play at least 200 snaps against the run. Just two — superstars Fred Warner and Nick Bosa — graded out among the top 130 league-wide (out of 191).
So an overhaul occurred. Out are De’Vondre Campbell (graded 131st), Leonard Floyd (143rd), Maliek Collins (181st) and Javon Hargrave, who played in just three games. In comes a youth movement. The 49ers spent each of their first five picks on defense, including four in the front seven.
- First-round EDGE Mykel Williams is a major athlete who graded out well against the run at Georgia. He’ll line up opposite Bosa to provide an immediate boost.
- Second-round defensive tackle Alfred Collins was the nation’s ninth highest-graded defensive interior player, per PFF’s.
- Third-round linebacker Nick Martin was fourth in all of FBS in tackles.
- Fourth-round defensive tackle CJ West was the nation’s 23rd highest-graded defensive interior player, including 11th against the run.
The 49ers have also brought back defensive coordinator Robert Saleh, who flamed out as Jets head coach but helped San Francisco become one of the elite defense in 2019 and 2020.
Collins and West are monstrous bodies in the middle who will likely play big roles right away. The 49ers also traded for pass-rush specialist Bryce Huff, who struggled to crack the Eagles’ rotation last year but had 10 sacks with the Jets in 2023.
It’s a defense with two stars and a lot of projects — both young projects and reclamation projects. That’s not just up front, either. San Francisco needs recent early draft picks like Renardo Green, Ji’Ayir Brown and Malik Mustapha (once he returns from a torn ACL) to step up. It’s a lot to ask, but the 49ers are hoping an improved front seven will take some of the pressure off.
Outlook: Can major changes lead to better results?
The 49ers experienced a massive, unprecedented roster exodus this offseason, one that was, frankly, necessary in part because many of those players didn’t live up to their billing and in part because the team needed salary relief. Plus, they paid Purdy.
The 49ers look different, and they feel different. While the core is still old, it’s not quite as old, and the 49ers hope they’re not as dependent on those players. On offense, that means Purdy improving and Pearsall stepping in and producing right away. On defense, the team will lean on recent draft picks rather than aging big names.
There is, simply, a lot more uncertainty with these 49ers. Their health should be better, but are the stars who got injured in 2024 still the same players pre-injury? They invested a ton of draft capital up front, but how many of those players are ready to be high-level contributors?
More than anything, the 49ers would like to return to the physical unit they were at their peak — a message Kittle himself mentioned earlier this offseason.
49ers betting odds
All odds via FanDuel Sportsbook.
Make playoffs |
-194 |
NFC West |
+165 |
No. 1 seed in NFC | +650 |
NFC Championship |
+900 |
Super Bowl |
+2000 |
The great teams have shown their abilities to pivot masterfully. The early Mahomes Chiefs were an explosive team that won high-scoring games. The more recent Mahomes Chiefs have leaned on a quarterback who’s become elite at making the right play and a defense restocked by superb drafting and under-the-radar free agent finds. The 49ers have certainly tried to emulate that path. Whether it works or not remains to be determined.
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