SANTA CLARA, Calif. — While San Francisco 49ers coach Kyle Shanahan and general manager John Lynch had long been preparing for the offseason exodus that hit their team in the opening days of free agency, linebacker Dre Greenlaw was one player they hoped to keep.

Although he played just 34 snaps in 2024 because of injury, Greenlaw had been integral to the 49ers’ defensive success since his arrival as a fifth-round pick in 2019. His combination of production and passion for the game made him the one in-house free agent — on a list that included key veterans such as cornerback Charvarius Ward, safety Talanoa Hufanga and guard Aaron Banks — whom the 49ers were willing to spend sizable money to retain.

Which is why, when news broke that Greenlaw had agreed to a three-year, $31.5 million deal with the Denver Broncos, Lynch and Shanahan did something they’ve never done before. After failing to sign Greenlaw before the negotiating window opened, Lynch and Shanahan flew to Texas to take one final swing at convincing Greenlaw to return to the only NFL team he’d ever known.

“We weren’t done with Dre, but we had to go through the process and other teams were aggressive in their pursuit of him and we were kind of, I guess, forced to be somewhat reactive when a market was set,” Lynch said of the last-minute plea to Greenlaw. “We just wanted to go have a conversation with our guy who we have a lot of respect and love for and we had a good discussion with him. He made a decision. We respect that decision.”

Greenlaw stuck by his agreement with the Broncos and departed San Francisco. While he long maintained his love for the 49ers and being a part of a tag team with fellow linebacker and close friend Fred Warner, he also sought the chance to be more of a defensive focal point.

Despite injuries that cost him 36 of a possible 100 regular-season games in his first six seasons, Greenlaw drew plenty of interest. The Niners hoped they could afford to keep him in an offseason in which they planned to dial back their spending and swallow significant salary cap hits to clean things up for quarterback Brock Purdy’s contract. But there would be no hometown discount from Greenlaw, which took his price well beyond any pre-free-agency offers the Niners made.

“We thought he was going to be highly sought after,” Broncos coach Sean Payton said. “I think the injuries may have played a little part as to how he became a free agent. Otherwise, he doesn’t ever hit the free agent market [and] he’s someone who is redone. … I wasn’t really surprised that there would be other teams heavily involved.”

That level of interest in Greenlaw didn’t catch the 49ers by surprise, but there was at least some expectation that his injury history might depress his market. In some sense it did, given that other, less accomplished (but healthier) off-ball linebackers signed for more money. The Philadelphia Eagles re-signed Zack Baun for $17 million per season, while the New York Jets retained Jamien Sherwood and the Kansas City Chiefs kept Nick Bolton, each at $15 million per year.

Still, the 49ers’ efforts to keep Greenlaw from free agency were fruitless because they weren’t close to where the market took him. When they finally did come up, it was too little, too late.

“It’s not just one player at a time,” Shanahan said. “You’re working 20 different things at a time. You’re trying to get a backup tackle; you’re trying to get a quarterback. You’re working on linebackers, you’re working on safety, you’re working on all these positions and they don’t just go in order negotiating with agents and these things happen. … We took another shot and we weren’t able to get it done.”

Linebacker has climbed higher on San Francisco’s lengthy list of needs entering the NFL draft later this month. Even if the 49ers had been able to keep Greenlaw, linebacker would have been a position of need; now it’s arguably one of the top three positions to address with their 11 selections.

Of course, replacing Greenlaw won’t be easy given all he has meant to the 49ers. In 64 regular-season games, the 49ers were 44-20 when Greenlaw played. They were 16-20 when he didn’t.

Speaking at the annual league meetings, Lynch and Shanahan indicated that third-year linebacker Dee Winters would get the first opportunity to step in for Greenlaw. In his first extended opportunity last season, Winters played 386 snaps in 15 games with 39 tackles and four pass breakups.

Winters’ speed and ability have intrigued the Niners since they used a sixth-round pick on him in the 2023 draft, but he struggled with injuries in 2024. He missed the first two games of the season with an ankle issue that lingered for much of the season and dealt with a concussion as well as neck and chest injuries.

According to Shanahan, Winters showed flashes of being a capable starter in 2024 and he has the right mentality to handle the job next to Warner, but it will be critical for him to add bulk to better withstand the rigors of the season.

“He plays to our style,” Shanahan said. “He loves to run and hit. I think he got a taste of that last year. … And now I think he’s just working on his body trying to improve so he can stay healthy and play the way that he does through a 17-game season. But he’s shown that potential and we’re bringing some competition here in the draft.”

Beyond Winters, they still have second-year linebacker Tatum Bethune and another third-year player in Jalen Graham. They also re-signed veteran Curtis Robinson and added linebacker Luke Gifford in free agency.

The draft, meanwhile, doesn’t appear to be loaded with talent at the position, though the 49ers have shown interest in plenty of prospects. Alabama’s Jihaad Campbell is considered the best player, but Georgia’s Jalon Walker could also play off the ball in base downs with edge rusher ability on passing downs. UCLA’s Carson Schwesinger, Oregon’s Jeffrey Bassa, South Carolina’s Demetrius Knight Jr. and Mississippi’s Chris Paul Jr. are other options expected to be available after the first round.

Regardless of how it plays out, the 49ers know it’s unfair to expect any player will be a one-for-one replacement for Greenlaw. It’s why they flew to Texas to try to convince him to stay, but couldn’t close the deal.

“We’ll see whether [failing to sign Greenlaw before free agency] was a good decision or not,” Lynch said. “That’s a high ask to go be Dre Greenlaw right away. We have the draft and so we’ll look at all positions and there, but there’s opportunity there.”