SANTA CLARA, Calif. — After an early June organized team activity, new San Francisco 49ers quarterback Mac Jones walked to a podium in the bowels of Levi’s Stadium and answered questions for about 11 minutes.

As Jones patiently responded to queries about everything from how he was nearly picked by the Niners in the 2021 NFL draft to why he believes coach Kyle Shanahan can get his career back on track, something was clearly nagging him.

On the practice field moments earlier, Jones had struggled, throwing an interception directly to cornerback Derrick Canteen and missing a handful of open receivers, including an overthrow to rookie wideout Jordan Watkins on a deep ball.

Throughout his media session, Jones alluded to his misfires on multiple occasions, opening a window into the first thing that he and the 49ers must fix as he steps into the No. 2 quarterback role behind Brock Purdy: rebuilding his ability to trust what he sees and cut it loose.

“My goal is to really just have great attempts like, you know, is the ball supposed to go there?” Jones said. “And if it is, then let it fly and be committed to it. Sometimes when you watch my film, it wasn’t a full commitment throw and I want to get better at that. … That’s the whole point of football is to try those throws, learn from them, and then when you get to the game you can say, ‘Hey, I can do this,’ or ‘I’m going to check this one down, you know, I’m trying to protect the ball.’ So, I’ve learned the hard way in a way.”

Indeed, Jones has taken a far more circuitous route to the red and gold of the 49ers than many observers would have expected when he entered the NFL out of Alabama in 2021. At the time, the Niners sent a trio of first-round picks and more to the Miami Dolphins to move from No. 12 to No. 3 to select their franchise quarterback.

Although Jones was widely regarded as the likely choice for most of the run-up to that draft, the Niners ultimately selected North Dakota State’s Trey Lance. Jones tumbled to the New England Patriots with the 15th pick.

As it turned out, neither Lance nor Jones would be the long-term answer for the Niners or Patriots, respectively, and both teams quickly moved on to other options. Jones was shipped to Jacksonville after a promising rookie season (56.9 QBR) gave way to a pair of disappointing years in which he posted QBRs of 38.4 in 2022 and 37.5 in 2023.

That one-year stop with the Jaguars offered Jones seven starting opportunities, with Trevor Lawrence injured, but he didn’t show many signs of improvement, posting a 39.8 QBR.

Jones set off into free agency for the first time in March and went searching for a chance to play for a coach who has a track record of squeezing the most from his quarterbacks.

Shanahan was the obvious choice in what felt for both sides like a pairing that was always going to happen at some point. At the outset of free agency, Jones and Shanahan texted, with Jones even joking that the pair “got in a huge fight” over the Niners’ original draft decision.

“The world works in mysterious ways,” Jones said, laughing. “I’m glad to be back here and learning from a great group of guys, and that’s players and coaches. So, you go where you go in the draft, right? You don’t get a lot of choice over that, but I’m definitely excited to be here now.”

Upon arrival in San Francisco, Jones went through an intensive course focused on fixing his fundamentals. For three weeks, Shanahan, offensive coordinator Klay Kubiak and quarterbacks coach Mick Lombardi went through cutups of Jones’ previous film, as well as tape of other signal callers showing Jones things like the footwork needed to succeed in the offense.

“To watch him go through those three weeks working on some technique things and just how we see football, I’m hoping it helps him and he enjoys it,” Shanahan said.

Rough practice days aside, enjoying his new place of employment hasn’t been a problem for Jones to this point. He’s made it clear that he likes being coached hard and that he’s craved the challenge that Shanahan and his staff have put before him.

Jones’ chance to learn the basics of Shanahan’s offense extends beyond the coaching staff.

In another fateful twist, when he was a young player at Alabama, Jones once played host for a recruiting visit by a young quarterback named Purdy. The pair spent that night in Tuscaloosa, Alabama, hanging out and playing video games, and though Purdy ultimately opted for Iowa State, Jones has enjoyed watching Purdy grow into the quarterback who recently signed a five-year, $265 million contract extension with the 49ers.

For Jones, Purdy offers a daily reminder of how developing in the right place with the right coaching staff can pay big dividends.

Before signing with the Niners, Jones also noted the ascent of Sam Darnold, another former high draft pick who struggled elsewhere, went to San Francisco and has since enjoyed success with the Minnesota Vikings and signed a sizable free agent deal with the Seattle Seahawks.

Despite Jones’ struggles elsewhere, the 49ers still see similar potential in him.

“He’s got a lot of traits that we like for a starting quarterback,” Kubiak said. “His career has kind of gone up and down a little bit the past couple years, but we saw the same things in Jacksonville that we loved about him as a college prospect, and that really excites us… I think Mac’s capable of being a starter in this league.”

For that to happen, Jones is going to have to rebuild from the ground up, starting with his confidence. Jones says it’s important for him to acknowledge what he could have done better in previous stops, and he intends to use those “scars” as motivation to improve.

In San Francisco, he’s the clear backup behind the unquestioned starter in Purdy. Whether he plays or not remains to be seen, though Purdy did miss a pair of games due to injury in 2024.

And if Jones needs to step in, Shanahan doesn’t want him to lament the interceptions thrown in practice or OTAs but remember those mistakes so he doesn’t make them again when it really counts.

“[If] you go through all these practices and you never throw a pick, you’re probably not getting better,” Shanahan said. “It’s hard when you get in that stadium and things like that. Not only are you getting hit for the first time, but now all that stuff counts and if you don’t let it rip and go through all that in practice, you’re not going to get any better in the games and then it’s usually a matter of time before someone passes you up.”