Who will be Kyle Shanahan’s QB reclamation project next year? 49ers mailbag

Readers love Mac Jones. They’re frustrated by Brandon Aiyuk.
And they’re curious about whether both are tradable this offseason and what the San Francisco 49ers might fetch in such a scenario.
Those are just some of the questions asked this week as the team prepares for a Monday game against the surprisingly solid Carolina Panthers.
Thanks for all the queries, which, as usual, have been slightly modified for length and clarity.
Who will be Kyle Shanahan’s quarterback rebuild project for next season? — Micah H.
Let me start by giving The Athletic editor Jimmy Durkin props for predicting the 49ers would add Mac Jones this past offseason. It seems like a no-brainer today, but Jimmy called his shot early on.
This year? Jimmy notes that Las Vegas Raiders quarterback Aidan O’Connell has a lot of Jones-ian qualities, including good anticipation (and not much running ability). The 49ers were sniffing around O’Connell before the 2023 draft. He’s still got one more year on his rookie contract, and the Raiders would have to release him for him to be available. But if they did, he’d make sense for San Francisco.
A bigger fish would be Zach Wilson, who was drafted one pick ahead of Trey Lance in 2021 and who’s scheduled to be an unrestricted free agent. The 49ers took a long look at Wilson that year because they were shopping for quarterbacks. He’s currently in Miami under Mike McDaniel, which means he’s already familiar with the Shanahan system.
Lance and former 49ers starter Jimmy Garoppolo also will be free agents, but, gee, I don’t see a reunion in the future. After the recent 49ers-Rams game, I watched Shanahan shake hands with Sean McVay and start heading toward the 49ers’ tunnel. His path took him directly in front of Garoppolo, and I wondered if they’d bro hug or at least shake hands or even acknowledge each other. They did not — it was like two ships passing in the night.
Would Mac Jones stay with the Niners next year if the only option is to be a starting QB on a struggling/rebuilding team? — Hugo G.
Very doubtful. Struggling/rebuilding teams are almost always the ones that trade for quarterbacks. If I’m Jones, though, I’d want to go where a Shanahan disciple calls the plays or where they run a version of his offense. Where does McDaniel wind up in 2026? What about Bobby Slowik? Does a team try to hire Klay Kubiak away from the 49ers or Klint Kubiak from the Seahawks?
A rebuilding team should look closely at:
- Trading for Jones
- Hiring a Kubiak to run the offense
- Signing Kendrick Bourne in free agency
That trifecta ought to get you off to a nice start.
How realistic is it that Brandon Aiyuk misses the entire season? It seems we are heading towards that path. How much more guaranteed money is owed to him? — Marcus B.
Every week, we begin Shanahan’s Monday press availability by asking: Will you open Aiyuk’s practice window this week? And every time Shanahan says no, but that it could happen at any week. The problem, of course, is that we’re running out of weeks.
As far as his contract, Aiyuk’s 2026 compensation of $26.2 million became fully guaranteed in April 2025. His salaries in 2027 ($27.3 million) and 2028 ($29.2 million) are not guaranteed. The structure of his 2025 and 2026 pay — most of which came via option bonuses — could make it difficult to move on without significant cap consequences. The 49ers would lose $14.2 million in 2026 cap space, which is almost double Aiyuk’s 2026 cap hit ($15.4 million), if they traded him before June 1.
As my editor, David DeChant, points out, the 49ers often buy insurance on these contracts, which could relieve some of the cap pressure. I have to think they got Aiyuk insurance after such a contentious negotiation.
Understanding we might not be alive tomorrow (throwback Shanahan-ism), where do you place the odds for the 49ers to move on from Aiyuk and Jones? What would be realistic compensation for those two? — Angel A.
For Jones, I think the chances are good, especially since the 2026 rookie quarterback class might be a dud. As far as compensation, it’ll depend on whether there are multiple bidders. The Raiders sent a late third-round pick to Seattle earlier this year for Geno Smith, but it’s hard to think there were other teams clamoring for him. My guess is Jones could fetch a second-rounder.
Aiyuk? His value is hurt by two things: last year’s three-ligament knee injury, and the fact that a team trading for him might have to take on a lot of salary. Maybe the 49ers could get an early Day 3 pick from a receiver-desperate team like Pittsburgh or Cleveland? They were interested in him 15 months ago.
Let’s go crazy here: The Niners are in a divisional-round playoff game on Jan. 18. Is Fred Warner — typically a three-month recovery for his injury — suiting up? — David L.
I’m dying to ask him that question. When I spoke to orthopedic surgeons about his injury, they said four months is more realistic for most people. Warner, of course, is not most people. I’m sure he’ll be lobbying to play as early as the opening round should the 49ers make the playoffs.
Is Anagram Fischer (AKA Christian McCaffrey) the type who adds to his already insane competitiveness by using the trade from the Panthers as motivation to remind them of their stupidity this Monday evening? — Matthew F.
I’ve gotta think he’s more thankful than vengeful about that trade.
Since trade:
49ers: 35-21 (playoff games: 6)
Panthers: 19-37 (playoff games: 0)
Will Nick Martin be starting now? — Bill H.
I’m not sure. The Panthers are second in the league in rushing attempts and have a couple of bigger-bodied runners in Rico Dowdle and Chuba Hubbard. Erstwhile strongside linebacker Luke Gifford’s been solid against the run so far. He wasn’t as good in coverage against the Rams’ three-tight-end looks.
Now that George Kittle is healthy and Luke Farrell has emerged recently, do you foresee the Niners employing any three-tight-end sets similar to what the Rams have done to add another dimension to the offense? — Brad A.
The 49ers have done a little of that — and have been successful — near the goal line. Shanahan also noted that while the team doesn’t technically have three tight ends on the field when Kyle Juszczyk is out there with Kittle and Farrell, the effect is similar.
“I know the Rams put those numbers up a lot these last couple weeks, but I think it all (comes down) to how a defense plays you,” he said. “I mean, if you want to get them in certain personnel groupings, it can help. You’ve got three guys on the field who can handle edges better, which usually gives you more space in the run game, but then you’ve got to see how one of those matches up versus a corner.”
How bad of an injury did receiver Jacob Cowing sustain? — Kevin L.
The bad news: Cowing said a couple of weeks ago that he’s suffered three aggravations of the hamstring strain he got on the first day of training camp. He said every time he hit top speed, the issue would reappear.
The good news is that he feels he’s gotten on top of it this time, and he’s close to returning to practice. Maybe he starts practicing in Week 15?
How has coach Brant Boyer been so successful in turning around the 49ers’ special teams? Is there a different scheme (is that a thing for special teams?), better players, simply better coaching? — Jason M.
He definitely brought in the right guys. Punter Thomas Morstead has been sharp, and (I don’t claim to be able to assess this, but people in the know say it) longsnapper Jon Weeks has been good, too. And, of course, Eddy Piñeiro has made all 22 field goal attempts. (The 49ers signed Matt Gay to the practice squad Wednesday as a temporary fill-in while Piñeiro recovers from his minor hamstring strain.)
It’s also clear that Gifford and Siran Neal are strong coverage players — Gifford popping out on kickoffs and Neal on punts. Boyer said he thought it would take several games for the unit to gel, and it looks like it’s doing just that.
How does the weekly schedule change when the 49ers play on Monday night, and how does it affect the following week’s schedule? — Clayton J.
Everything gets pushed back a day. The 49ers normally practice Wednesday-Friday. This week it’s Thursday-Saturday. Next week, they’ll have only one recovery day — Tuesday — before getting back at it Wednesday. Shanahan’s a big believer in sleep, so it’s possible the Wednesday workday will begin later than normal.
Eddy Piñeiro = Len Eshmont award? — Steve P.
Steve is referring to the 49ers’ MVP award as voted on by players. It’s certainly not out of the realm of possibility. Kicker Phil Dawson won the other MVP award — The Bill Walsh Award, voted on by coaches — in 2015. I’d say McCaffrey is the safer bet for the Eshmont, which is the more prestigious of the two awards. Piñeiro’s probably competing with Trent Williams, Dee Winters and Kittle for the other.
Now even the Niners’ kicker is injured? What is in the water in their locker room? — Shawn W.
Think of it this way: By this point last year, the 49ers had two kicker injuries (Jake Moody and Matthew Wright). So they were 100 percent worse in that department last season.




