SANTA CLARA, Calif. — Mike Singletary can see it in Alex Smith’s eyes, in his body language. He’s a different player now. Confident. Mature. Experienced.

At all of 25, Smith has been at the top and at the very bottom during his short NFL career. There was all the hype and talk of his potential when the San Francisco 49ers chose him No. 1 overall in the 2005 NFL draft.
Three years later he had disappeared, having worked his way back from shoulder surgery only to get hurt again three days before last year’s season opener. He missed all of 2008.
“Alex is a totally different guy today than he was even six months ago,” Singletary said Wednesday. “I think his mindset is clear.”
On Sunday, Smith gets to start over, given a second chance — a rare thing in professional sports these days.
San Francisco’s game at Indianapolis will mark his first start since Nov. 12, 2007, and it just so happens the Colts are also the team he faced in his NFL debut back in ’05.
“I think it’s just coincidence I’m back starting again against the team I got my first start against,” Smith said.
He is taking this all in stride, but it’s clear he’s thrilled to be the top guy again after all this time.
“Back on the podium,” Smith said with a smile Wednesday, the standard day for the starting quarterback to address the media. “I missed it the most.”
Smith missed this so much he opted to stay with San Francisco last spring rather than leave for a potentially better situation and more money elsewhere. He said at the time he wanted to finish what he started, to redeem himself. He never lost belief he could be a starting quarterback for this franchise. Now, others may begin to regain faith in him, too.
Singletary has, that’s for sure. Even when the coach named Shaun Hill the starter during training camp.
The 49ers need Smith’s leadership on offense now like no other. They have endured six straight losing seasons. They’re 3-3 and have lost two straight games on the heels of a 3-1 start, though Smith nearly led them back from a 21-0 deficit in a 24-21 defeat at Houston last Sunday.
In March, Smith agreed to a restructured contract that sharply reduced his base salary.
Smith was due to make nearly $10 million this season under the deal he signed in 2005. The 49ers now have Smith under contract through next season at a salary more commensurate with his four up-and-down years with the club. Smith isn’t all about the money. He said everything he’s endured has given him a new perspective and appreciation that he gets to play football for a living.
“To me he’s been a true team player, the ultimate team player, through this process,” Singletary said. “The thing that spoke volumes to me about him was in the offseason he had a chance to move on and go to another team and make more money. But he decided to stay because he felt that he wanted to be a part of what was here. He wanted to finish what he started. I’m excited for him going forward and I’m not going to build too much into it. I’m going to let Alex’s play speak for itself.”
This season marks the first time Smith has been fully healthy since shortly after his promising 2006 season in which he took every snap for the 49ers, throwing for 2,890 yards and 16 touchdowns. His shoulder problems began with a sack early in the 2007 campaign and later stoked a periodic feud with former coach Mike Nolan that seriously hampered both men’s careers. Nolan questioned how hurt Smith really was on several occasions, shocking behavior from an NFL head coach.
Smith seems to have forgotten all of these bad memories, or at least pushed them out of mind.
He has stayed ready, though he never knew when he might get another shot.
“This is the NFL. If you’re a backup quarterback and think you’re not going to play, you’re kind of in a dreamland,” Smith said. “How many QBs go through a season and take all of the snaps and can handle that? It’s a lot. You have the mindset, you have to have the expectations to play. The question is, when does it come? You have to be ready for that because you don’t know when it’s going to come.”
Smith isn’t making too much of his promotion, knowing full well how quickly things can change in this league. If he doesn’t perform, Singletary might decide to make another switch, even though the coach said this won’t be a “flavor-of-the-month kind of thing.”
Smith’s teammates are proud of his turnaround. They all know it’s not often someone gets to revive their career with their original organization, but rather is forced to start over elsewhere with a clean slate.
Smith took over for Hill in the second half against the Texans on Sunday and completed his first six passes on the way to a 15-of-22 day for 206 yards. He threw three touchdowns to tight end Vernon Davis.
“I always believed in Alex,” Davis said. “Sometimes it takes certain guys a little longer to come around. He always had the tools but it just took him some time. He’s always had it.”
Smith doesn’t think he’s changed to get to this point, even if others notice differences in his relaxed demeanor.
“I don’t think I ever lost confidence. It had been two years almost since I’d been in a live game,” Smith said, noting preseason games aren’t the same as the real thing. “It probably comes from a little bit of everything. Being around the game more, you know more about it, a better understanding of it. The last couple of years put things in perspective for me, especially with football and what is important, what you really miss when you get away from it.”