49ers cutting cord on Brandon Aiyuk, envision Gus Bradley as next defensive coordinator

SANTA CLARA — Brandon Aiyuk’s sketchy status hovered like a dark cloud over this past 49ers’ season, and that won’t be the case next season.

“It’s safe to say he’s played his last snap with the Niners. It’s unfortunate, a situation that went awry,” general manager John Lynch in Wednesday’s end-of-season address with coach Kyle Shanahan.

As that 49ers’ power couple enters its 10th season, they are aligned in so much about this direction’s franchise, and neither is willing to tolerate Aiyuk’s uncertain status, as evident a month ago when the former No. 1 wide receiver was placed on the reserve/left squad list.

Aiyuk’s recovery from a 2024 knee injury seemed to be progressing, but his failure to stick with the 49ers’ recovery plan allowed them with his consent to void $27 million in 2026 guarantees. Aiyuk visisibly remained around the team and in warmups through training camp and the preseaosn, then went AWOL in September.

“I wish I knew (why). Can’t help you,” Lynch said.

Shanahan said his line of communication with the 2020 first-round pick ended once Aiyuk did not respond to Shanahan’s repeated attempts to reach him, as well as other team members.

“Eventually there was not much of an explanation, so it’s hard for us to understand and not something I’ve seen in 22 years of coaching,” Shanahan said. “It’s unfortunate, and it’s confusing for all of us.”

Shanahan and Lynch touched on several topics during their 30-minute session, including:

BRADLEY NEXT DC?

Shanahan confirmed that Gus Bradley, this season’s assistant head coach/defense, is the frontrunner to step in at defensive coordinator as Robert Saleh leaves to coach the Tennessee Titans.

“I’m going to say it’s a wide net but Gus is the obvious one to everybody, and us too,” Shanahan said. “We will go through the whole process and the requirements we want to do, too. Hope it’s sooner than later.”

Shanahan said he expects Saleh to try poaching some coaches from his staff and that will be worked out in the coming days.

Shanahan is going on his fifth different defensive coordinator in five seasons, adding: “I would love to go on vacation and not make my family wait. … I’m very happy for Saleh, and he gets what he deserves.”

MAC JONES TRADE?

Neither Shanahan nor Lynch seemed excited about flipping backup quarterback Mac Jones into trade equity, although neither ruled out a deal, with Jones under contract for 2026.

“We’re not into getting rid of good players. So I’d be surprised if Mac wasn’t around us next year,” Shanahan said.

Added Lynch: “Mac made this place better and was outstanding this season. He picked us up in a huge way. It was a really fun process to watch him come in and the joy he was playing with. … Like Kyle said, you always listen (to trade offers), but I know we’re a better team with Mac Jones on our roster.”

SUBSTATION SPECULATION

Lynch did not outright dismiss this month’s viral conspiracy alleging that 49ers’ injuries could be traced to a neighboring electrical substation. Lynch isn’t buying it, either.

“Because it deals with allegedly the health and safety of our players, you have to look into everything. Our guys have been,” Lynch said. “We’ve been reaching out to anyone and everyone to see if a study exists, other than a guy sticking an apparatus underneath the fence and coming up with a number that I have no idea what that means. We’ve heard that debunked. We’ll look into it.

“… I know a lot of games have been won at this facility since it opened (in 1989). We won’t turn a blind eye. We’ll look into everything.”