SANTA CLARA >> Kyle Shanahan will have a batch of new coordinators in 2025, including the promotion of Klay Kubiak to offensive coordinator, even as Shanahan continues to call the 49ers’ plays in his upcoming ninth season.

More changes are coming after a 6-11 last-place season, even if they aren’t as major as finding the replacements for Nick Sorensen as defensive coordinator and Brian Schneider as special teams coordinator.

One “priority position” remaining constant is Brock Purdy at quarterback, presumably with a contract extension he wants signed by the 49ers’ spring workouts in mid-April.

“What we know about Brock is he’s our guy,” Lynch said while sitting aside Shanahan in Wednesday’s news conference. “We have interest in Brock being around here for a long, long time. He’s done so much for our organization and won big games.”

Purdy is entering the final year of his rookie deal, and he could command an annual salary in the NFL’s top pay grade, between $50 million and $60 million. He went 13-13 in his past 26 regular-season starts, but he led two NFC playoff comebacks last season to reach the Super Bowl, where the 49ers fell in overtime to the defending champion Kansas City Chiefs.

“Brock is the leader of our team. I’ve loved these three years with Brock. I plan on being with Brock for the time I’m here,” Shanahan said. “... We’re capable of winning a Super Bowl with him, and we almost did. And I know he’s capable of it in the future.”

While those ringing endorsements can and will be used against the 49ers in Purdy’s contract negotiations, the more urgent matter is for Shanahan to name a new defensive coordinator for the fourth time in five years. Thanks to the 49ers’ failure to go on a deep playoff run, more candidates abound than when Shanahan hired Steve Wilks in 2023 or promoted Sorensen last year.

Shanahan confirmed that Brandon Staley is an option to replace Sorensen after joining the 49ers this past season as assistant head coach who worked with defensive backs. External candidates could include Robert Saleh, Shanahan’s defensive coordinator from 2017-20, and Jeff Ulbrich, a former 49ers linebacker and Saleh’s replacement as the New York Jets’ interim coach this season.

As for personnel changes, Lynch said he expects the returns of left tackle Trent Williams and wide receiver Deebo Samuel. Defensive tackle Javon Hargrave, who suffered a torn triceps and played in just three games this season, will be released with a post-June 1 designation. Lynch hopes free agency leads to the return of both Hargrave and linebacker Dre Greenlaw.

Lynch bluntly stated that Samuel remains under contract ($16 million cap charge in 2025), adding: “He’s done a ton for this organization. We’re not in the business of letting good players out of here.”

Williams is expected back after a bruised ankle joint that Lynch said has “taken a positive turn.” It shelved the star left tackle for the final seven games, and he missed out on his 12th straight Pro Bowl and fourth straight All-Pro team.

“Trent’s mindset is where it always is and he’s interested in still being a great player and has a lot in the tank.”

The 49ers’ inability to close out three NFC West games still had Shanahan steaming after the season. They coughed up fourth-quarter leads in losses to the Rams (Weeks 3 and 15), the Cardinals in Week 5, and the Seahawks on Nov. 17.

“A lot of our finishers weren’t out there,” Lynch said, alluding to the 49ers’ mass injuries. “On top of it, we still had opportunities and still put ourselves in good position and couldn’t get it done. We have to own that as a team.

“We have high expectations. It’s our job to fix that. Kyle and I are as committed as ever to doing just that.”

One player who wasn’t committed: linebacker De’Vondre Campbell. He refused to come off the bench in the second half of the Dec. 12 loss to the Rams.

“That’s something we don’t roll with,” Shanahan said. “It’s hard to stomach, and once we saw it, we were done with it.”

Also tough to digest were the relentless miscues on special teams. When a reporter suggested Shanahan has an apparent disregard for that unit, Shanahan took exception. Lynch intervened to defend his coach of eight seasons, then Shanahan noted how they invested in special teams via free agency and draft picks, only to see injuries to kicker Jake Moody and punter Mitch Wishnowsky impact an already troubled unit.

“You can’t change the whole thing out, and Brian ends up being the fall guy for it,” Shanahan said.

Near the end of Wednesday’s farewell session, Shanahan and Lynch heaped praise on their growing bond, with their ultimate goal still being to win the Super Bowl, which will be played at Levi’s Stadium next season.

The road to that game can’t possibly repeat this year’s, in which personal turmoil besieged the 49ers, including the Aug. 31 shooting of top draft pick Ricky Pearsall (“It was a huge success for him this year,” Shanahan said) as well as the loss of children by Williams and Charvarius Ward.

Said Lynch: “This is a production-based business. We’re paid to win games and compete for championships. One thing I will say, acknowledging we fell short of that standard, I am proud of this team. ... I will say this season I’ve never had anything like it based on the amount, the severity, the unique circumstance, and I was proud how our team stuck together and had each other’s backs.”