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San Francisco 49ers defensive coordinator Steve Wilks speaks to reporters before the NFL football team's rookie minicamp in Santa Clara, Calif., Friday, May 12, 2023. (AP Photo/Jeff Chiu)
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San Francisco 49ers defensive coordinator Steve Wilks speaks to reporters before the NFL football team’s rookie minicamp in Santa Clara, Calif., Friday, May 12, 2023. (AP Photo/Jeff Chiu)
Dieter Kurtenbach
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Steve Wilks is not a scapegoat for the 49ers losing the Super Bowl.

The 49ers defensive coordinator’s exit was set in motion long before Sunday’s loss in Las Vegas, and I’m not even sure winning the game would have saved him.

It wasn’t working. It wasn’t going to work. And instead of pretending that things would get better with time — instead of trying to save face after making a bad hire — Kyle Shanahan made the right decision on Wednesday to fire Wilks.

Shanahan is used to losing coaches, but that’s because they’ve been hired for better jobs by other teams. This is the first high-profile firing of Shanahan’s tenure.

But it had to happen.

The fruit of the Shanahan coaching tree has been so over-picked that the Niners’ head coach had to go outside the building to hire the third defensive coordinator of his tenure.

Wilks had been one-and-done in his prior four jobs. His prior three gigs — Browns defensive coordinator, Mizzou defensive coordinator, Panthers secondary coach — ended with him being effectively fired.

There’s nothing ambiguous about this firing. He’s now one-and-done in his last five gigs.

To be clear, the Super Bowl didn’t help Wilks’ cause. Yes, Patrick Mahomes failed to drive down the field to a touchdown in regulation, but Wilks made some baffling defensive calls late in the fourth quarter and in overtime, opening the door for Mahomes to take advantage.

The Niners had succeeded throughout the game by consistently rushing four and dropping seven into zone, mixing single and two-high coverage. It was basic stuff, but it worked because the Niners’ defensive line was having a huge game.

And then, when the tension was highest, Wilks decided to start running more man-to-man looks.

Mahomes, flummoxed to that point in the game, couldn’t believe his luck. Against a steady, now-predictable diet of super-soft zones on early downs and man-to-man on late downs, he quickly drove the Chiefs into position for a game-tying field goal (forced by the Niners defense, which dropped into zone near the goal line). He moved down the field for the game-winning touchdown in overtime with relative ease.

But that was only the most recent reason Wilks was fired.

The issues started in training camp, when it became clear to Niners players and staff that Wilks wasn’t keen on melding his system — a basic, secondary-first scheme, circa 2005 — with the Niners’ defensive-line-first attack.

Some not-so-subtle nudging came Wilks’ way from Shanahan and general manager John Lynch before the season even started.

But even in late October, Wilks admitted that he was still learning the Niners’ system (which, itself, isn’t terribly complicated.)

By then, Wilks had already been pulled out of the coach’s box and onto the sideline in an effort to increase communication with players. But most of the time, when the defense was off the field, Wilks was off to the side, sitting by himself, looking at his tablet.

Throughout the season, players endorsed Wilks in only light ways.

There were a lot of references to him being a “great guy” or “smart coach.”

Yet you never heard any evidence given to those claims. It certainly wasn’t evidenced on the field. And I would not label Wilks with either description from my admittedly limited (by comparison) interactions with him.

I’ve learned more than I’ll ever be able to remember from on- and off-the-record conversations with football coaches over the years. In most cases, they can’t help themselves from teaching. But that never happened in Wilks’ press conferences or any side conversations I had with him. At his best, he was boring. At his worst, he was terse and condescending. (Shanahan can be both, too, but at least the evidence of his excellence as a coach is apparent on the field.)

You have to wonder if personality was an issue for Wilks when coaching this team.

Regardless, Shanahan made the same kind of “great guy” claims Wednesday during an unscheduled media conference call, announced 10 minutes before its start.

“[It was] a tough decision. It really says nothing about Steve as a man or as a football coach. He’s exactly what we wanted as a man. He is a great football coach. But just where we’re going, where we’re at with our team from a scheme standpoint… I felt pretty strongly that this was a decision that was best for our organization,” Shanahan said.

But would a truly great coach have found himself in such a position?

Wilks knew the deal when he took the job: The Niners had the No. 1 ranked defense in the NFL in 2022, with even more talent coming onto the roster in 2023.

Wilks’ job was to take what was already established — a foundation that landed two different defensive coordinators head coaching jobs — and maintain it. It’d be even better if he could make it better, perhaps with his outside experience.

He failed at his only objective.

Wilks deserves credit for helping cornerbacks Charvarius Ward and Deommodore Lenoir have their best seasons in the secondary. His banging of the table to draft safety Ji’Ayir Brown was an excellent decision, too.

But Wilks inherited a defense with four other Pro Bowl players, and the unit unquestionably regressed. The Niners added Randy Gregory and Chase Young mid-season to improve the pass rush — both players were massive disappointments this season.

So focused on the secondary, Wilks could never marry the pass rush to the pass coverage on the 49ers’ defense. Arguably the NFL’s most talented defensive line struggled to pressure quarterbacks throughout the season — teams could swiftly pick the coverage apart, beating the pass rush to the punch, or add protection to extend plays and beat a secondary that had no scramble-drill plan.

Having inherited the best linebacker duo in the game, Wilks often utilized Fred Warner as a de-facto safety in Tampa 2 coverage — a look that was better suited for the game during the first decade of the century, not the third.

With Warner 30 yards away from the line of scrimmage, is it any surprise the Niners’ run defense slipped to the middle of the pack, and was exploited in the final weeks of the regular season and the two NFC playoff games?

That’s when this decision to fire Wilks was undoubtedly made.

And while Shanahan said he stewed over it for the last few days, there was no sane world where Wilks returned.