But as the 49ers regroup from their latest postseason disappointment and begin to retool for another attempt at securing their first Super Bowl triumph in three decades, they have already signaled their intentions to not simply maintain the status quo and hope things work out better next time.

Coach Kyle Shanahan announced Wednesday that the team had fired defensive coordinator Steve Wilks. The dismissal did not come entirely without warning, given that the 49ers experienced some growing pains on defense during the regular season after Wilks took over for DeMeco Ryans, then struggled on that side of the ball during the NFC playoffs. But it certainly qualified as surprising that a team would make such a major change to its coaching staff three days after coming so close to winning the Super Bowl.

“We felt pretty strongly that this was a decision that was best for our organization,” Shanahan told reporters, according to the team’s website. “Even though it was one I didn’t want to make, it was something that I realized. … A different direction is what’s best for [the] organization.”

The 49ers hired Wilks after the Houston Texans hired Ryans as their coach last offseason. Ryans had served as the 49ers’ defensive coordinator for two seasons after taking over for Robert Saleh when the New York Jets hired Saleh as their coach following the 2020 season.

Wilks was coming off a stint as the interim coach of the Carolina Panthers. He made a strong bid to be retained as the full-time coach. But he was passed over last offseason by Panthers owner David Tepper, who hired Frank Reich instead — only to fire Reich 11 games into this season.

Wilks, formerly the coach of the Arizona Cardinals, joined the racial discrimination lawsuit filed against the NFL and teams by Brian Flores, the former coach of the Miami Dolphins, in February 2022. Last March, U.S. District Judge Valerie Caproni ruled Wilks’s claims against the Cardinals must be submitted to arbitration under the authority of NFL Commissioner Roger Goodell, based on the terms of his employment contract.

With Wilks in charge, the 49ers ranked eighth in the NFL in total defense during the regular season. They had led the league in total defense in the 2022 season under Ryans. Shanahan criticized an ill-fated all-out-blitz call by Wilks during an October defeat to the Minnesota Vikings, part of a three-game skid for the 49ers following their 5-0 start. Wilks said at the time he wished he could “take it back.” Wilks made an in-season move, at Shanahan’s urging, to call the defensive coverages from the sideline rather than from the coaches’ booth.

The Green Bay Packers and Detroit Lions totaled 52 points and 318 rushing yards combined against the 49ers during the NFC playoffs. In the Super Bowl, the 49ers mostly played well on defense, limiting quarterback Patrick Mahomes and the Chiefs to 19 points — on four field goals and a touchdown that resulted from a muffed punt by the 49ers — in regulation.

But in overtime, after the 49ers took the ball first and got a field goal, they allowed the Chiefs to drive for a winning touchdown. Shanahan called a timeout during the Chiefs’ decisive drive, acknowledging later that he didn’t like the 49ers’ defensive “look” on the play while also expressing the belief that the 49ers’ defensive players were weary.

Standout pass rusher Nick Bosa told reporters Tuesday that the 49ers “had some issues throughout the year” on defense but were “playing our best ball at the end.”

By Wednesday, Shanahan was announcing the change. Shanahan said he was making the move to try to give the team its best possible chance next season, in his view, and suggested that Wilks’s successor might be someone familiar with the 49ers’ defensive scheme from the previous few seasons before Wilks’s arrival.

“When you have a group of guys who have played at a high level doing certain things a specific way for a while, I do feel that’s the best thing to do for them,” Shanahan said. “But if I find something that I believe in and it can be sold on that could be a better avenue, I would never hesitate to do that.”

The 49ers have reached four of the past five NFC championship games. But they have lost two Super Bowls — both to the Chiefs — and two NFC championship games over that span.

They remain without a Super Bowl victory since January 1995, when George Seifert was their coach and Steve Young was their quarterback. This is the franchise that once considered Super Bowl triumphs its birthright. It is the team of Bill Walsh, Joe Montana and Jerry Rice.

These 49ers keep getting close. General Manager John Lynch and Shanahan were hired in 2017. By the third year of their regime, they had built an annual contender. The roster remains one of the most talented in the NFL. The 49ers will have to deal with salary cap issues this offseason, given the star power on their roster and the accompanying cap impact of those players’ contracts. But they do have quarterback Brock Purdy on a cap-friendly rookie deal at least.

“Obviously we’re hurting,” Shanahan said Sunday night in Las Vegas. “Our team’s hurting. But that’s how it goes when you put yourself out there. I’m real proud of our guys. No regrets with our team. I thought our guys played so hard today. Not everything was perfect, by no means. … We’ll take some time. We’ll get over this and come back next year ready to go.”