There really is a lot that seems inexplicable about the 49ers’ fall this season.
San Francisco was the top team in the NFC last year. It clinched the top seed in the conference with a 12-4 record before resting many of its starters for the final game of the regular season.
After 12 games this season, the 49ers are 5-7 and barely holding onto a mathematical chance of returning to the postseason.
Stay in the game with the latest updates on your beloved Bay Area and California sports teams! Sign up here for our All Access Daily newsletter.
They have struggled on special teams throughout the season. That cannot be debated.
And while the offensive and defensive total-yardage numbers are not too far off from a year ago, there are two areas in which the team has taken a precipitous drop.
The 49ers have fallen off considerably in scoring from last season. They are scoring a touchdown per game fewer on offense while giving up a touchdown more on defense.
In both cases, it can be traced to poor play within the red zone. The 49ers’ defense ranks 31st in the NFL, giving up touchdowns on 70.7 percent of the opposition’s trips inside the 49ers’ 20-yard line.
San Francisco 49ers
Find the latest San Francisco 49ers news, highlights, analysis and more with NBC Sports Bay Area and California.
The drop has been even more significant on offense. Last year, the 49ers’ red zone production was best in the NFL. They scored touchdowns on 68 percent of their red-zone opportunities. This season, the 49ers rank 27th at 48.9 percent.
The biggest reason for the 49ers’ drop can be traced to Christian McCaffrey, Brandon Aiyuk and Deebo Samuel.
Last season, those three playmakers combined for 40 touchdowns.
McCaffrey, the NFL’s Offensive Player of the Year, had 14 touchdowns rushing and seven receiving.
Samuel added 12 touchdowns (seven receiving, five rushing), and Aiyuk caught seven touchdown passes.
Through 12 games, those three have combined for just two touchdowns. Samuel produced both touchdowns (one receiving and one rushing).
And Samuel is the only one of those three who can add to that touchdown total over the final five games of the regular season.
Aiyuk and McCaffrey are on season-ending injured reserve. Aiyuk’s season came to an end when he sustained a torn ACL in his right knee against the Kansas City Chiefs in Week 7.
Less than two months after signing a lucrative contract extension, Aiyuk’s season came to an end with 25 catches for 374 yards and no touchdowns.
McCaffrey missed the first eight games of the season due to Achilles tendinitis. He was back on the field for 3 1/2 games this season. He had 50 carries for 202 yards and no touchdowns while catching 15 passes for 146 yards. He did not get into the end zone, either.
McCaffrey’s season came to an end on Sunday night when he sustained an injury to the posterior cruciate ligament of his right knee against the Buffalo Bills.
McCaffrey vowed to return to form in 2025.
“I’ll work smarter and harder than ever to come back better from this,” he wrote on a social media post.
Meanwhile, Samuel has not picked up the slack with Aiyuk and McCaffrey missing significant action. Samuel, who is signed through the 2025 season, is in the midst of a down season.
Samuel is third on the team with 38 catches for 531 yards and one touchdown. He has been ineffective as a rusher, carrying 27 times for 79 yards and one touchdown.
While there might be some mystery as to why the 49ers have fallen so far so fast, their offensive woes are easy to understand when considering what has happened to three of their top offensive playmakers.