Why the 49ers’ pass defense has fallen apart — and can it be fixed?

Over the last four weeks of the 2019 season, the 49ers’ formerly dominant defense has taken multiple hits. Can this be solved?

From Weeks 1-12 of the 2019 season, only the New England Patriots could claim to have a better pass defense than the San Francisco 49ers, and that’s only because the 2019 Patriots were (and are) playing pass defense at a historically great rate. But the 49ers, led by defensive coordinator Robert Saleh, weren’t far off. From Weeks 1-12, San Francisco allowed opposing quarterbacks to post a QBR of 72.50, and only the Patriots were better at 50.55. The 49ers allowed a Positive Play Rate (plays in which the Expected Points Added were above zero) of 37%, and only New England was better at 36%. Per Sports Info Solutions, the 49ers’ defense saved 188.5 points below the average, and opposing offenses had minus -140.3 EPA against them. Again, only the Patriots were better in either category.

No defense allowed fewer completions (198) or passing yards (1,854), and though there was a vulnerability in touchdowns allowed (11), matching the interception total with 11 seemed to make that problem go away. The 49ers were 10-1 after 12 weeks, their only loss in overtime to Seattle, and the defense was the biggest part of that success equation.

Then, regression happened in a big hurry. The 49ers went 2-2 in their next four games, including a Week 15 loss to the Falcons that put everybody on alert. Losing 20-17 to the Ravens is one thing, but allowing Matt Ryan to complete 22 of 34 passes for 234 yards, two touchdowns, and no interceptions in a 29-22 stunner? Well, that’s not the act of a top defense. And over the last month, the 49ers’ defense has been anything but.

San Francisco has had a Positive Play Rate of 49% in that time. Their opposing QBR allowed has jumped to 102.39. They’ve saved 15.3 points above the average (the Packers have led the league in that time at 81.1), and their EPA of 24.3 is the fifth-worst in football, behind the Lions, Jaguars, Raiders, and Giants. They’ve allowed 95 completions for 987 yards, 10 touchdowns, and just one interception over that 2-2 stretch. Basically, the team that will take the field once again against the Seahawks this Sunday in hope of gaining the first overall seed in the NFL playoff picture has a defense playing like you’d expect from a team awaiting a top 10 slot in the draft.

Pass rush has certainly been a problem. From Weeks 1-12, San Francisco led the NFL with 45 total sacks, and 4.09 sacks per game. And while they were in the middle of the pack in quarterback hits (71) and hurries (109), the extent to which Nick Bosa and his buddies on the defensive line were able to demolish the intentions of enemy quarterbacks went a long way to disguising those other numbers.

Over the last four weeks, it’s been a very different story. San Francisco is tied for last in the league with the Browns and Seahawks with just three total sacks, and though they’ve kept the hits and hurries going to the point where the team’s overall pressure percentage has gone up from 29.67% to 31.06%, those pressures are not leading to breakups of big plays. Quite the opposite.

And as is the case with most Legion of Boom-style defenses, this one doesn’t blitz a lot. The 49ers have the fourth-lowest blitz percentage in the NFL at 20.3%, which was fine when they were getting home with just four defenders. But that’s not happening now, and the pressure/coverage schism is negatively affecting both sides at the worst possible time.

Injuries have also played a factor. That the 49ers’ pass defense has declined severely at the time time the team has been missing safety Jaquiski Tartt is absolutely no coincidence. Tartt suffered a broken rib in the team’s Week 13 loss to the Ravens, and the hope is he’ll be back for the Seattle game. He’s been the team’s best safety this season, allowing just 13 catches on 25 targets for 98 yards and one touchdown all season, and the efforts of Jimmie Ward and Marcell Harris have not matched up.

In the last four weeks of the 2019 season, 49ers defensive coordinator Robert Saleh has struggled to keep up with injuries, and opponents keying on vulnerable tendencies. (Tommy Gilligan-USA TODAY Sports)

Saleh was also without Richard Sherman after the veteran cornerback suffered a hamstring strain against the Saints in Week 14, missed the Falcons game, and returned in Week 16 against the Rams. Sherman has been one of the five best cornerbacks in the NFL this season, clamping down on enemy receivers, so the absence of these two great players would go a long way to explaining the current malaise. Not to mention the losses of edge-rusher Dee Ford, who’s been out with a hamstring issue since Week 14, and linebacker Kwon Alexander, who was lost for the regular season to a torn pectoral in early November.

The result of all this? Plays like this 10-yard touchdown pass from Jared Goff to receiver Brandin Cooks in San Francisco’s 34-31 win over the Rams last Saturday. Cooks gets free to the left uncontested, linebackers Fred Warner and Dre Greenlaw bite on Goff’s boot-action, and three defenders follow Robert Woods on his crossing route. Cornerback Ahkello Witherspoon gets close near the end of the play, but not close enough. When this defense isn’t reading correctly, there isn’t really a lockdown scheme, or a current group of healthy players, in line to make up for it.

Warner’s 46-yard interception return for a touchdown near the end of the first half was one example of how this defense works as it’s supposed to. The four-man line compresses the pocket, forcing Goff to make an off-platform throw. Warner reads the quick pass to running back Malcolm Brown all the way, and that’s that.

There is another vulnerability the 49ers defense has, and opposing offensive coordinators are starting to go after them heavily to attack it.