What looked like a contender in August flatlined by December. The 49ers went 6–11, finished last in the NFC West, and missed the playoffs for the first time since 2020. Injuries piled up. Depth got exposed. And now, everything’s on the table — from how Kyle Shanahan builds his roster to how the team handles wear and tear.

And just as the 49ers were supposed to bounce back, they’re falling apart before the new season training camp has even begun. What started as a quiet contract standoff with wide receiver Jauan Jennings has now exposed much deeper fissures in Kyle Shanahan’s roster. In a team already reeling from a bottom-of-the-division finish, Shanahan, who already has a ton of problems to deal with, has fallen victim to another negative development. Something only he can figure out how to deal with.

According to David Lombardi, the 28-year-old Colton McKivitz is engaging in a strategic hold-in, attending team events but withholding full participation to apply quiet pressure. McKivitz signed a one-year extension last season worth $5.85 million and received $3.785 million in new guarantees. And like Jennings, McKivitz is now entering a year where he’s expected to perform at a high level for below-market pay. Lombardi wrote, “It’s not just Jauan Jennings. Colton McKivitz is in a similar contractual spot — lame duck year, underpaid relative to 2024 performance — that demands some of the 49ers’ attention.”

McKivitz started 17 games in 2024 and allowed just two sacks despite San Francisco’s broader struggles in pass protection. His performance was steady, nothing elite, but certainly dependable on a line that lacked it. McKivitz is now entering a lame-duck year where he’s expected to perform at a high level for below-market pay. The 49ers’ offensive line depth is thin, and the McKivitz dilemma can cause heavy damage to the team that Shanahan just can’t afford. Lombardi quotes Shanahan on the issue. The HC said, “We’ll do everything we can to make that work out, but it’s not always easy.”

Injuries have haunted the 49ers like a curse in recent seasons, and just days before training camp, that dark cloud refuses to lift. In a gut punch to an already tense offseason, the team has placed six players on the active/physically unable to perform (PUP) list, including star wideout Brandon Aiyuk and promising rookie Ricky Pearsall. For a franchise desperately trying to regain stability, the timing couldn’t be worse. Training camp hasn’t even kicked off, and Kyle Shanahan’s roster is already limping into battle.

But while McKivitz’s situation poses a serious threat to the offensive line, the roots of the 49ers’ current tension can be traced back to an already simmering standoff—one that started with wide receiver Jauan Jennings. Troubles are piling up for Shanahan; one must wonder when he will find some relief.

Kyle Shanahan and the Jauan Jennings dilemma

Wide receiver Jauan Jennings is at the center of it all. After putting up career-highs with 77 receptions, 975 yards, and 6 touchdowns, Jennings believes he’s outplayed his current deal, and he might be right. Jennings is entering the final season of his two-year, $15.4 million contract with the 49ers and is seeking a long-term extension before the start of the 2025 season. GM of the 49ers, John Lynch, praised Jennings after he passed a physical when he reported for camp this week. He said, “I anticipate him being out there. You guys know our feelings on JJ. He embodies what we think a Niner is all about. He plays the right way and we love him. We’re not going to get into the contract talks and all that. That takes care of itself. We love him and he’s here.”

Even Shanahan couldn’t keep his emotions away from the business end of the game as he shared his thoughts not only on Jennings’ but also on McKivitz’s contractual situation with the 49ers. He also revealed that Jennings hasn’t formally requested a trade, and Shanahan wants both Jauan and Colton to stay and reach an agreement. He said, “The way they feel about us is the same way we feel about them. That’s the easy part. The hard part is the business side.”

The San Francisco 49ers find themselves at a critical crossroads. What began as a quiet contract hold-in by Jauan Jennings has now spotlighted deeper roster instability, with Colton McKivitz’s unresolved situation threatening to unravel the offensive line. The team wants to avoid any distractions this year, and as Kyle Shanahan attempts to navigate this growing tension, his own words, “we’ll do everything we can to make that work out, but it’s not always easy,” capture the uncertainty looming over the team. If the front office fails to address these internal contract issues swiftly, the 49ers’ hopes of a bounce-back season could collapse before it even begins.