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Deebo Samuel emerged down the stretch of the 49ers' Super Bowl run. He won't be available to help them start another.

San Francisco's promising second-year wide receiver is having surgery Thursday to repair a broken foot and is expected to miss 12-16 weeks, NFL Network first reported.

Samuel suffered a Jones fracture on Tuesday during a throwing session with teammates in Nashville, Tennessee. The team later confirmed Samuel underwent a procedure on his left foot Thursday.

Samuel could miss up to a handful of games to start the season given his reported timeline.

It's a big blow for a 49ers team that figures to contend for the league crown again, and a player who battled injuries throughout his college career.

Samuel proved to be a vital piece in just his first season in the Bay, catching 57 passes for 802 yards.

Only All-Pro tight end George Kittle posted higher totals. The rookie's 14.1 yards per catch led all 49ers receivers with at least 15 receptions. His contribution in the run game was comparably valuable to the league's No. 2 scoring offense, as he carried the ball 14 times for 159 yards and three touchdowns.

Samuel tallied 127 receiving yards and 102 rushing yards over three playoff games, including 92 yards from scrimmage against the Chiefs in the Super Bowl. His absence will put a greater onus on head coach Kyle Shanahan to employ a promising but unproven cast of wide receivers.

With Emmanuel Sanders off to New Orleans, Kendrick Bourne (30 receptions, 358 yards) is the 49ers' next-leading returning wideout. San Francisco will also look for contributions from 2020 first-round pick Brandon Aiyuk, 2019 third-rounder Jalen Hurd, who missed his entire rookie season with a back injury, and possibly Dante Pettis, who's caught just 38 passes over his first two seasons.

We'll be watching for more on this post surgery, but assuming the longer end of that potential timeline seems wise.

And nothing is certain here.

Rehabbing for 12 weeks would last until Sept. 10, while 16 weeks would last all the way to Oct. 8. The 49ers are set to open their regular season on Sept. 13 against the Arizona Cardinals.

Samuel himself believes he will be ready well before that. The second-year pro tweeted that he will be back in 10 weeks, and be better than ever.

If only it were that simple.

As NBCSports.com noted, the break occurs between the base and shaft of the fifth metatarsal on your foot. Jones fractures often times are seen as one of the worst possible injuries for a football player to get.

In August 2018, research in the Orthopaedic Journal of Sports stated "50 percent of all players with a previous Jones fracture demonstrated incomplete healing. Moreover, position-specific performance scores over the first 2 years of a player’s career were lower across all positions for those with fractures compared with controls."

This came from reviewing every player who attended the NFL Scouting Combine between 2009 and 2015.

The 49ers know all about the dangers of Jones fractures, too. Receiver Trent Taylor sustained the injury in training camp last year. He suffered multiple setbacks, underwent five surgeries and missed the entire 2019 season.

Sammy Watkins, who was the No. 4 overall pick in the 2014 NFL Draft, had a Jones fracture in May 2016. He was coming off a season where he had 1,047 receiving yards and nine touchdowns. It took Watkins two years to get fully back to health, and he has averaged only 595 receiving yards in the three seasons since the injury.

While Samuel is optimistic, this obviously is a big blow to the 49ers. All they can do now is hope this isn't another Taylor situation, and that Samuel can return to the field at full strength.

Stay tuned.