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The San Francisco 49ers are in relatively unfamiliar territory. They’re struggling to effectively stop the run.

The team’s defense, which has ranked among the NFL’s top two in run defense in each of the past two seasons and hasn’t finished outside the top 10 since 2018, is ranked No. 23 in expected points added (EPA) per play against the run. The 49ers have fared even worse against designed runs, ranking No. 25 in EPA/play when quarterback scrambles are discounted.

The 49ers are in the bottom-right quadrant, which means they have a good pass defense (second-best in the league) but a below-average run defense: pic.twitter.com/2kfr7LpZsO

— David Lombardi (@LombardiHimself) October 16, 2023

Such runs accounted for essentially all the damage on the ground against the 49ers in their recent 19-17 loss to the Cleveland Browns, who amassed 160 yards on 34 carries. Running backs Jerome Ford and Kareem Hunt ripped off big gains at critical moments that enabled Cleveland to wrestle away control of the game.

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It marked the most rushing yardage that the 49ers had allowed since the Atlanta Falcons racked up 168 against them last season. That, too, ended in a loss for the 49ers. But they had a better reason for their struggles in that game because seven of their defensive starters were hurt and unavailable by the end of it.

Coach Kyle Shanahan was openly critical of the run defense after watching Sunday’s game tape.

“I was disappointed in it,” he said. “I’m not sure the exact stat compared to the others, but if I had to guess, it was our most missed tackles on the year.”

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Shanahan was correct. The 49ers’ 10 missed tackles, per Pro Football Focus, were more than the nine they missed over the previous three games combined.

“I thought they got our edges way too much, just blocking down on our D-ends and getting around,” Shanahan said. “We played a lot more two-shell defense, and when you play two-shell defense, you’re a little bit behind in the run game. But we’ve been able to stop guys pretty good that way. When they got our ends and we didn’t get our safeties downhill, they bled us out too much. And when you add on a couple of those missed tackles and everything, it was way too much.”

The absence of starting 49ers linebacker Dre Greenlaw, who missed the game with a hamstring injury, seemed to play a part. Defensive end Nick Bosa said the 49ers failed to match Cleveland’s intensity in the battle for control of the run game. Greenlaw, of course, has been a spark plug for the team’s defense. Shanahan expects him back at practice this week.

Opponents have rolled out a consistent formula against the 49ers defense this season. They’ve focused on the quick passing game to lessen damage from the 49ers’ pass rush, and they’ve strived to steadily run the ball to establish a threat that opens the immediate space necessary for those throws. The 49ers play an aggressive, penetrating Wide 9 technique along the defensive line that the Browns outfoxed with screens and traps.

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“They schemed us up pretty good,” Bosa said. “They got the edge on us, which is something we take pride in — setting edges and turning things back into the teeth of the defense. They did a really good job scheming us up. Definitely a learning experience of how teams are going to attack us, especially teams who know our scheme because (their defense) runs a similar scheme.”

Can the 49ers correct course? Their recent history has seen some sporadic struggles against the run that the defense has indeed fixed. Last season’s team bounced back from its struggles against Atlanta after it was fully healthy again. The 2021 squad was shaky to begin the season against the run, but Arik Armstead’s midseason move from defensive end to tackle spearheaded a surge up the rankings.

By now, opponents have developed a streamlined formula to attack the 49ers defense. Not every opponent has been successful, but the Los Angeles Rams (No. 6 EPA/play in the run game), Arizona Cardinals (No. 9) and the Browns (No. 17) have delivered significant yardage on the ground against the 49ers.

“When their team has over 300 yards of offense, teams are going to look at what hurt us,” linebacker Fred Warner said. “Lots of screens and perimeter runs.”

But the Cleveland run that might’ve vexed the 49ers the most came up the middle, late in the fourth quarter. The Browns ran a trap to Ford, and 49ers defensive tackle Javon Kinlaw fell for it. He fired off the line and into the backfield, essentially untouched, only to see Ford bolt right by him on the way to a 22-yard gain. Warner tried to clean up the mess, but he couldn’t fully reach around 374-pound Cleveland right tackle Dawand Jones. It’s fair to wonder if Greenlaw would’ve fared better against Browns left tackle Jedrick Wills, who eliminated 49ers linebacker Oren Burks from the play.

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Ford’s run also forced a missed tackle from cornerback Deommodore Lenoir. It put the Browns in range for what’d be the game-winning field goal and left the 49ers with a sour taste in their mouths because their goal was to force backup Cleveland quarterback P.J. Walker to beat them.

“Especially when you’ve got a quarterback coming in who hasn’t started yet, the best way to make that guy uncomfortable is to take away the run game, and with 160 yards in that, we obviously didn’t,” Shanahan said. “That was disappointing, especially on those last two drives.”

On Monday night, the 49ers will face the Minnesota Vikings, who have the No. 22-ranked run game by EPA/play. They’ve lacked explosiveness on the ground. But the Vikings rank No. 5 in rushing success rate — which measures the percentage of runs that yield a positive EPA — and that indicates they’ve done well to eliminate negative plays and give their quarterback, Kirk Cousins, a workable platform for success.

The 49ers’ defensive blueprint begins with taking that platform away. Choking off the run game is a surefire way to tilt dynamics in favor of a pass rush that ranks No. 15 in NFL with just 15 sacks — and not for a lack of talent. Doing so will be imperative for the 49ers as they progress further into this season because many of their chief rivals have showcased strong run games. The Seattle Seahawks rank No. 2 in rush EPA/play. The Philadelphia Eagles rank No. 3. That means the time for improvement is now before a critical three-game stretch against those teams arrives next month.

The 49ers often repeat the mantra of Arden Key, one of their former defensive linemen who helped unlock the resurgence of the team’s defense in 2021.

“Stop the run,” Key would tell his teammates, “and we can have some fun.”

Those words ring especially true now, with the 49ers’ run defense in an obvious need for a fix.

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(Top photo of Kareem Hunt running in for a touchdown: Gregory Shamus / Getty Images)

“The Football 100,” the definitive ranking of the NFL’s best 100 players of all time, goes on sale this fall. Preorder it here.

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