Projecting what the 49ers will do with Mac Jones long term

He’s 3-0 and playing well, but it’s early

San Francisco 49ers quarterback Mac Jones (10). | Kirby Lee-Imagn Images

Do the 49ers have a quarterback controversy?

It’s getting some talk, but three games in is too small a sample size. Week to week, Mac Jones is likely to start until Brock Purdy is 100% healed from his turf toe injury. Once both are healthy? That depends on the 49ers' record under Jones and the plans of Kyle Shanahan, who is not known for his loyalty to quarterbacks.

Three scenarios exploring if Jones could become the 49ers' long-term starter: why it doesn’t happen, how it could, and what the Niners are likely to do.

Why it doesn’t happen

San Francisco 49ers quarterback Brock Purdy (13). | Darren Yamashita-Imagn Images

Start with the contract. The Niners agreed to a no-trade clause with Purdy. Then in the trade market, who wants him at this price? Under a hypothetical where the Niners look into moving on, can they trade Purdy? Go through the league, remove the teams who like their starter or the young quarterback in development, or are likely to have a top-ten pick to take a QB. 

In my view, the only teams left standing are maybes, Pittsburgh if Aaron Rodgers retires or leaves, and Carolina if they want to move off Bryce Young. Some could argue Cleveland, but the Browns aren’t going to deal for a quarterback that struggles in bad weather.

Unless Purdy is told point blank, you are no longer the starter, I see him using his no-trade clause to reject a move.

If the Niners can’t move Purdy but start Jones, then they are paying a $265 million contract to their backup QB. Not viable. Jones can only become the long-term starter if Purdy exits stage left. For this season though, contracts are locked in, Shanahan will start who he thinks gives the Niners the best chance of winning.

End with Purdy’s history. A Super Bowl appearance and a top-5 finish in the MVP voting. That can be countered with what Purdy has done since the Super Bowl, and he’s vulnerable in that debate. However, he holds three aces with the contract, the no-trade clause, and an empty trade market.

Even if the Niners were to find a trade partner, and Purdy waives his no-trade, they’d have to pay part of the contract to move him, and trade him at a bargain rate. The Yorks would not be pleased with any of that.

How it could happen

San Francisco 49ers quarterback Mac Jones (10). | Gary A. Vasquez-Imagn Images

First, Jones needs to continue at this pace and play the best football of his career well into the season. Three games in, he’s been excellent, but can he stay healthy? Will he fall off?

Based on what we’ve seen so far this season, Jones is proving himself and starting to realize the potential of a first-round pick. But it’s just three games, and the Niners live under an injury cloud.

Why would Shanahan take Jones over Purdy? Several factors. Fastest to get the ball out, average time to throw Purdy 2.9, Jones 2.6 for the season, and according to some reports, 2.24 in the Rams game. That’s a necessary skill when the Niners run game is anemic and they have to throw this often.

Less dependence on the run game to succeed. When the Niners run under 80 yards in a game, Jones is 3-0 while the rest of the Niner QBs are 3-18 under Shanahan  — this from AP’s Josh Dubow.

More velocity. Jones can throw into tighter windows to beat good coverage and improve efficiency in the red zone.

Two-minute drill. Jones excels; Purdy is good, not great. Per Kyle Posey of Niners Nation, Jones is 5-for-5 on scoring drives in two-minute/overtime possessions when the 49ers had sufficient time to score.

Fewer turnovers. A point of emphasis by Shanahan. Purdy keeps saying he needs to be smarter with the ball, but nothing changes. Eight interceptions for Purdy in his last five games.

Purdy has a clear advantage in escapability and as a scrambler. He has mastered the offense. The locker room trusts him implicitly.

All of that factors in, but if Shanahan decides his best chance at a ring is with Jones, then in theory he could act to make that happen. He’d have to convince Purdy to waive his trade clause, the Niners would need to find a trade partner, the Yorks would need to sign off on paying part of his contract to enable the deal, and then the Niners would sign Jones to an extension. In theory, that’s possible, but in reality, it’s a big stretch.

The alternative path is the Niners signing Jones to a multi-year extension for a lot more money. Keep both quarterbacks, and then cut Purdy after 2027. Again, possible but unlikely.

What the Niners are likely to do

San Francisco 49ers head coach Kyle Shanahan. | Darren Yamashita-Imagn Images

Keep Purdy through 2027, keep Jones through 2026, and then let Mac walk to get the comp pick. If they won’t move off Purdy, you can argue then deal Jones after this year; you’d get a lot more back than a comp pick.

True, but that’s not how Shanahan thinks. He would only have Jones for a year under that scenario. He’d rather have Jones for two and a lesser draft pick. Fans can object to that decision, but Shanahan has final cut on the roster.