SANTA CLARA >> Mac Jones, four years after the 49ers bypassed him with the No. 3 overall draft pick, is finally heading to coach Kyle Shanahan’s offense, a league source confirmed Wednesday night.

Jones is coming in as the No. 2 quarterback, that is, behind incumbent starter Brock Purdy, who is still awaiting what’s expected to be a team-record contract extension within the next two months.

After three years with the New England Patriots and last season with the Jacksonville Jaguars, Jones agreed to join the 49ers on a two-year, $7 million deal with $5 million guaranteed and a maximum value of $11.5 million, according to the NFL Network.

Jones was considered a favorite for the 49ers’ No. 3 overall pick in 2021 before they veered instead for Trey Lance, who spent two years with the team before they traded him before the 2023 season to the Dallas Cowboys; Lance is now a free agent.

Regardless of Purdy’s pending financials, the 49ers needed to restock their depth chart behind him. Last year’s backups, Brandon Allen and Josh Dobbs, became free agents earlier Wednesday, and Dobbs had agreed Monday to a two-year deal with the Patriots, who moved on from Jones and drafted Drake Maye a year ago with the No. 3 overall pick.

Jones made it to the Pro Bowl his rookie season with New England, going 10-7 and posting what have been the best statistics of his career (67.6 completion percentage, 3,801 yards, 22 touchdowns). That 2021 season ended with a wild-card playoff loss to the Buffalo Bills, and more 17 losses followed against just eight wins in Jones’ starts over the next two seasons.

Jones, a Jacksonville native and University of Alabama product, went 2-5 as the Jaguars’ starter finishing the season in place of an injured Trevor Lawrence. The Jaguars recently reached a deal with former 49er Nick Mullens to serve as a backup this season.

Purdy is entering the final year of his rookie contract, at a salary of $5.35 million. However, he and the 49ers’ brass have expressed a mutual desire to hatch a long-term contract, and general manager John Lynch confirmed two weeks ago that negotiations are underway.

The only other quarterback on the 49ers’ roster is Tanner Mordecai, who spent most of last season on the practice squad as an undrafted rookie.

Jones, by virtue of his position and even his Pro Bowl accolade, is the 49ers’ highest profile addition in what’s been a grueling opening days of free agency.

The 49ers, 13 months removed from the Super Bowl, have seen 11 players leave and join other teams, including Wednesday’s official trade of wide receiver Deebo Samuel to the Washington Commanders.

Others to leave: Dobbs, linebacker Dre Greenlaw (Broncos), cornerback Charvarius Ward (Colts), left guard Aaron Banks (Packers), safety Talanoa Hufanga (Broncos), defensive end Leonard Floyd (Falcons), offensive tackle Jaylon Moore (Chiefs), running back Elijah Mitchell (Chiefs), and, on Wednesday, defensive tackles Javon Hargrave (Vikings) and Maliek Collins (Browns). Fullback Kyle Juszczyk was informed Monday of his release after eight seasons and having served last year as the 49ers’ longest-tenured player.

The 49ers have yet to confirm the reported acquisitions in free agency of wide receiver Demarcus Robinson (Rams), tight end Luke Farrell (Jaguars), linebacker Luke Gifford (Titans), cornerback Tre Brown (Seahawks) and safeties Jason Pinnock (Giants) and Richie Grant (Falcons)

Re-signed were guard Ben Bartch, running back Patrick Taylor Jr., defensive tackle Kevin Givens and linebacker Curtis Robinson.

Another player released Wednesday was safety Juan Thornhill by the Cleveland Browns, prompting a Fox Sports report that Thornhill will visit the 49ers today. He played four seasons with the Kansas City Chiefs before calf injuries hindered his two-year tenure with the Browns.

Both Hargrave and Collins secured two-year deals within 10 minutes of their release, which both came with post-June 1 designations for salary cap purposes.

Hargrave, according to multiple reports, promptly hooked up with the Minnesota Vikings on a $30 million deal with $19 million guaranteed. Collins’ two-year, $20 million pact is with the Cleveland Browns, with $13 million guaranteed.

One player not arriving in free agency is defensive end Joey Bosa, who agreed to join the Buffalo Bills (one year, $12.6 million) rather than join his younger brother Nick on the 49ers.

The flurry of 49ers departures pits them with $86 million in dead cap money for 2025 and $21.5 million in 2026, according to The AP’s Josh Dubow.