Five biggest questions for the 49ers as they hunt for embattled star’s replacement

As the NFL offseason officially kicks off Monday morning, it comes with one of the more exciting times of the year.

The NFL combine is set to take place at the end of February, where players unexpectedly shoot up draft boards due to insane athletic potential. Then comes the draft from April 23-25, where Indiana quarterback Fernando Mendoza is expected to be the Raiders’ top choice for new coach Klint Kubiak.

Following the hire of former Rams OC Mike LaFleur to be the head coach of the Cardinals — his brother, Matt, is the head coach of the Packers — a record-tying 10 new coaches will begin the 2026 season.

Among the most shocking was John Harbaugh going from the Ravens to the man leading Jaxson Dart, Cam Skattebo and the Giants. Chargers DC Jesse Minter then replaced Harbaugh in Baltimore. Mike Tomlin called it quits in Pittsburgh, and the Steelers quickly pivoted to Mike McCarthy.  

The 49ers were bitten by the head coaching vacancies as defensive coordinator Robert Saleh left for the Titans.

Here are some of the bigger questions that need to be addressed by the 49ers.

What happens to Brandon Aiyuk?

In one of the more public breakups seen in a while, Brandon Aiyuk and the 49ers appear headed for an ugly divorce this offseason.

Aiyuk never played in 2025 after recovering from a torn ACL in 2024. According to reports, he stopped showing up to the facility and then posted a video of himself on social media driving as high as 111 mph near Levi’s Stadium in December.

It’s expected the 49ers will move on from Aiyuk, ending a tumultuous time with the young star.

Do they need to search for another backup QB?

One of the best assets a team can have is a capable backup quarterback, and the 49ers learned that lesson last year when Mac Jones thrived.

As entrenched starter Brock Purdy went down with an injury, Jones kept San Francisco’s season alive with impressive play. In 11 games, he threw for 2,151 yards and 13 touchdowns (six interceptions) while completing 69.6 percent of his passes.

With multiple teams needing a starting quarterback this upcoming year, Jones is seen as a potential target for multiple teams. However, according to reports, the 49ers have no desire to trade Jones. Even with Purdy as the starter, Jones has proven himself a very capable backup, and that’s valuable in today’s game.

How does Raheem Morris replace Robert Saleh?

When Saleh headed out of town to be the head coach of the Titans, head coach Mike Shanahan was left looking for a new leader of the defense.

It was an easy decision as he wasted no time in choosing former Falcons head coach Raheem Morris. They spent time together throughout their careers, most recently in Atlanta in 2015-16.

While Morris is considered one of the better defensive minds in the NFL, Shanahan is looking for some consistency from the position.

Morris is the fifth defensive coordinator in five years for San Francisco as they’ve gone from DeMeco Ryans to Steve Wilks to Nick Sorensen to Saleh and now Morris.

For the 49ers to reach their goal next year, the defense must take a step forward.

Substation rumor or real?

In one of the craziest rumors of the offseason, there’s a viral conspiracy theory that the electrical substation near the 49ers’ training facility and Levi’s Stadium is the cause of San Francisco’s biggest issue the last few seasons.

Health.

One of the most injury-plagued teams in the league over the past few seasons, GM John Lynch is at least considering all theories after season-ending injuries to key players — most notably linebacker Fred Warner and defensive end Nick Bosa — have become the constant theme the past few years.

“Because it deals with allegedly the health and safety of our players, I think you have to look into everything,” Lynch said. “We’ve been reaching out to anyone and everyone to see, does a study exist other than a guy sticking an apparatus underneath the fence and coming up with a number that I have no idea what that means? That’s what we know exists. We’ve heard that debunked. … The health and safety of our players is of the utmost priority.

Who knows what comes of it, but at least the 49ers are doing something.

And with the No. 27 pick in the NFL Draft, the 49ers select…

San Francisco should be targeting a wide receiver as early as possible in the draft.

As noted earlier, Aiyuk will be gone, but the 49ers’ depth is expected to take a massive hit.  

Jauan Jennings and Kendrick Bourne, the two who played leading roles this year, are both free agents in the offseason. Second-year wide receiver Ricky Pearsall showed flashes of becoming a reliable pass catcher, but consistency and injuries continued to slow down his development.

Tight end George Kittle is recovering from a torn Achilles, which means Shanahan and co. need to give Purdy some more options, and addressing that need through the draft is a great way to start.