General manager Trent Baalke said Wednesday that the 49ers have extended an "olive branch" to Smith to stay with the only NFL team he has ever known. All that started before the league locked out the players in the ongoing labor dispute.
The Sacramento Bee cited multiple sources last week in reporting that the 49ers offered Smith a one-year contract to return before the league year ended. Now Smith can't sign with San Francisco -- or any other team -- until the labor situation is settled and free agency begins.
"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 worked with 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 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 overall pick in next week's NFL draft and likely will 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 their facility.
Harbaugh didn't specifically talk about Smith but said he looks for certain tangibles 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 Harbaugh hasn't had the opportunity to study Smith in person, there's plenty of recent history to revisit.
Smith took over the 49ers' starting job midway through 2009 and was entrenched as the starter heading into last season. After the quarterback separated 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 victory over the eventual NFC West champion Seattle Seahawks. After a flop at San Diego, Singletary turned back to Troy Smith for a must-win Dec. 26 game with the St. Louis Rams.
That 25-17 loss cost the coach his job with one week to go. Jim Tomsula, serving a one-game stint as interim head coach, went with Alex Smith for a win over the Arizona Cardinals in the season finale.
The 49ers finished 6-10, leaving them without a winning season since their last trip to the playoffs in 2002. Still, with limited options this offseason, San Francisco is 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."
The Associated Press contributed to this report