This piece originally appeared in our twice-weekly sports newsletter Section 415. Sign up for the newsletter here and subscribe to the Section 415 podcast wherever you listen.
The 49ers’ greatest strength is now their biggest weakness, their biggest weakness is suddenly a clear strength, and their best, most dependable player is out for the remainder of the season.
The team is 4-2 and still tied for first-place in the NFC West despite a wave of crushing injuries, but almost nothing about this team makes sense.
Since the beginning of Kyle Shanahan’s tenure in Santa Clara, the 49ers have consistently ranked among the NFL’s best rushing teams. The 2022 acquisition of Christian McCaffrey supercharged an offense that already ran the ball effectively, as the former Stanford star led the NFL with 1,459 rushing yards in 2023.
Even when McCaffrey missed 13 of the 49ers’ 17 games last year, the team still finished 12th among 32 teams with 127.2 rushing yards per game. From the early days of a Tevin Coleman-Matt Breida-Raheem Mostert rotation to Jordan Mason and Isaac Guerendo’s work as McCaffrey’s fill-ins last season, the 49ers have averaged at least 100 rushing yards per game for eight consecutive seasons and ranked in the top half of the NFL in rushing yards in seven consecutive years.
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In 2025, their 82.2 yards per game ranks 30th and McCaffrey hasn’t cracked 70 yards in a game yet.
The 49ers have offset their inability to run the ball by generating points in other ways, namely on Eddy Piñeiro’s long field goals. The team’s new kicker, signed after Jake Moody’s Week 1 miscues, has drilled all 15 of his attempts including four from beyond 50 yards.
Special teams, outside of Robbie Gould’s tenure as the kicker, have been a nightmare under Shanahan. This season, the coverage and return units have plenty of room for improvement, but Piñeiro has been so reliable that the idea of games coming down to a last-minute field goal attempt is actually appealing to the 49ers.
The 49ers need Piñeiro to remain reliable in large part because their depth chart has been decimated. Brock Purdy has missed four games, George Kittle has been sidelined for five, and Nick Bosa is out for the season. Now, the Shanahan-era ironman, Fred Warner, is out for the season after undergoing surgery to repair his dislocated ankle on Tuesday.
49ers fans are accustomed to watching their team without key players, but no one knows how this defense will perform without Warner, who has started 121 of 122 regular-season games since he entered the league in 2018. The 49ers haven’t looked like the version of a team we’ve become accustomed to under Shanahan’s lead, and with Warner out, there’s no chance they will.
Their one constant is gone.
Before the season began, Shanahan signaled the team was entering a new phase.
“It’s a different window,” he told The Standard’s Tim Kawakami.
He believed this because the 49ers extended their quarterback on the richest deal in team history, cut veteran players to maintain flexibility under the salary cap, and went all-in on young talent including a massive rookie class that will be counted on to anchor future playoff runs.
Still, the differences from prior iterations of Shanahan teams to the version we’ve watched in 2025 is stark. Six games in, even the coach would probably admit the 49ers are too reliant on their passing game, too dependent on field goals, and too green on defense to win the division.
Yet here they are, with 11 games to go, still in control of their own destiny. Nothing makes sense about these 49ers, but at least for a fleeting moment, that’s OK.