General manager Trent Baalke said Wednesday that the 49ers have extended an "olive branch" to Smith to come back to the only NFL team he has ever known. All that started before the NFL locked out the players in the ongoing labor dispute.
Smith can't sign with San Francisco — or any other team — until the labor situation is settled and free agency begins.
New coach Jim Harbaugh already has expressed confidence in Smith as a quarterback in his system, and Baalke made it clear that the 49ers made an offer for the free agent to return.
"It's up to Alex to make the decision on whether he wants to be a 49er again," Baalke said. "I think Jim's made it clear. We've made it clear through the process that the olive branch has been extended."
A call to Smith's agent, Howard Skall, and an email to the quarterback seeking comment weren't immediately returned.
Smith was demoted and promoted several times last season and has had a different offensive coordinator every year since coming out of Utah. He has fallen out of favor with fans — many of whom have booed him on several occasions — and has failed to lead the 49ers to the playoffs.
With the lockout canceling offseason workouts, postponing free agency and threatening training camp, San Francisco is at a disadvantage perhaps more than most teams. David Carr is the only quarterback on the roster, and asking a rookie to take the reins with a shortened offseason could be even more difficult.
The 49ers have the No. 7 pick in next week's NFL draft and will likely take a quarterback at some point.
Team president Jed York, speaking on a conference call forum with some 5,000 fans Wednesday night, had a little fun with the idea of Harbaugh's NFL playing history.
"If we don't have a quarterback at least our head coach has been a quarterback in the league and we might suit him up for a couple of games. Jim has been working out hard," York said. "Obviously the quarterback position is the most important position on the field and (Trent and Jim) are going to figure out who the best guy is. They said today they'd like Alex to be in the mix, but it's up to Alex to decide if he wants to be here."
While fans have wavered on Smith's ability to lead San Francisco, Baalke believes the quarterback's experience in the West Coast offense — which Harbaugh plans to run — and his time with the team make him a valuable option in an offseason of uncertainty.
"He understands this building. He understands the system that coach is interested in running," Baalke said. "From a dynamic standpoint, they obviously hit it off in their discussions. There's a lot of comfort in having somebody, especially in the situation we're in where there are so many unknowns."
Harbaugh, hired away from Stanford in January to replace the fired Mike Singletary, hit the field for a local pro day Wednesday featuring some 50 players — his first time in a formal group practice situation. Dressed in a gray 49ers hoodie, black sweats and a black cap, Harbaugh greeted prospective draft picks on the final day the team could host players at its facility.
He didn't specifically talk about Smith, but said there are certain tangibles he looks for in a quarterback.
"Guys that can win, guys that can figure things out, guys that really have the DNA to be quarterbacks," Harbaugh said.
While he hasn't had the opportunity to study Smith in person, there's plenty of recent history to revisit.
Smith took over the starting job midway through 2009 and was entrenched as the starter heading into last season. After separating his non-throwing left shoulder Oct. 24 at Carolina, then-coach Singletary turned to 2006 Heisman Trophy winner Troy Smith for the next five games — even after Alex Smith was healthy again.
Troy Smith went 3-2 as a starter, then it was Alex Smith's turn again for two games, including a commanding win over eventual NFC West champion Seattle. After a flop at San Diego, Singletary turned back to Troy Smith for a must-win game with the Rams on Dec. 26.
That 25-17 loss cost the coach his job with one week to go. Jim Tomsula, serving a single-game stint as interim head coach, went with Alex Smith for a win against Arizona in the season finale.
San Francisco finished 6-10, leaving the 49ers without a winning season since their last trip to the playoffs in 2002. Still, with limited options this offseason, the 49ers are open to seeing what Smith can do under Harbaugh's direction.
"I don't know how to keep beating the drum on this: Coach is very comfortable with him. I'm very comfortable with him," Baalke said. "Will Alex choose to come back here? You'll have to get him on the phone and ask him that question. He's certainly a guy we would like to throw into the mix."
AP Sports Writer Janie McCauley contributed to this story.