The San Francisco 49ers were used to losing coaching staff pieces. Under Kyle Shanahan, they seamlessly transitioned from Robert Saleh to DeMeco Ryans. So when Ryans got the Houston Texans head coaching job last offseason, there was an expectation that it would happen again. And don't get me wrong, the 49ers still have a relatively strong defense under Steve Wilks.

But relatively strong is not exactly strong. Or at least not dominant as it had been under Saleh and Ryans. The 49ers lost to the Kansas City Chiefs, missing another chance at a Super Bowl ring. They have been to three consecutive NFC Championship Games, two Super Bowl losses in four seasons. This time around, though, the defense was not one of the biggest qualities of the team.

Ultimately, that’s why 49ers’ head coach Kyle Shanahan decided to fire Wilks.

“It just ended up not being the right fit,” Shanahan mentioned when explaining the reason to move on, adding that Wilks’ system didn’t align with what San Francisco had run before.

Disconnect

In 2021, Shanahan chose an internal replacement for Saleh, promoting linebackers coach DeMeco Ryans. Last offseason, though, the head coach didn't see an obvious replacement inside the building and looked for external options.

Steve Wilks, who finished last season as the Carolina Panthers’ interim head coach, was the choice. Being from the outside, with a different schematic philosophy, Wilks would naturally bring change and factors that Shanahan would only completely understand during the season — a less controllable environment compared to the previous transition.

After the week 7 loss to the Minnesota Vikings, Shanahan publicly complained about a zero blitz call at the end of the first half.

"I have no problem with zero blitzes, especially when people need a lot of yards,” Shanahan said after that game. "If you need to get 20 yards to kick a field goal, I have no problem with a zero blitz. But I do when there's 16 seconds left. That's where he lost track. There was no necessary need for that just because of the time. I have no problem with that play call, but when it's that time, you can't do that. That's not an option."

It's a pretty tough way to handle the situation. But it was not the only public demonstration of dissatisfaction. After the bye, Kyle Shanahan decided that Steve Wilks would go from the booth to the sideline, calling plays just like his predecessors had done.

Performance

The 49ers still had a really good defense — fourth by DVOA, for example. But it was simply not as good as it had been. In EPA/play, the Niners were 10th in the regular season — down from fifth in the two seasons under Ryans.

The biggest difference, though, is a defensive philosophic shift. Under Saleh and Ryans, it was a front-based defense, which allowed the pass rush to shine and the run defense to dominate. With Wilks, it's a secondary-based system. In a vacuum, this is fine, but it's not perfect considering how the 49ers defensive roster is built. Their front players are the dominant ones, and the secondary doesn't have top-end pieces outside of Charvarius Ward.

With that approach, the run defense suffered. The 49ers were 1st in rush EPA between 2021 and 2022. In 2023, they have fallen all the way down to 26th.

And that was a big issue in the playoffs. Despite wins over the Green Bay Packers and Detroit Lions, San Francisco allowed big games from Aaron Jones and David Montgomery. The team allowed 21, 31, and 25 points in the playoffs. It’s not bad, for sure, but it’s also not doing what Shanahan thinks complementary football is about.

The 49ers’ championship window is still open to a certain degree, but the defense needs to play at an elite level to finally put them over the top, and it didn’t happen in the 2023 season.

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