Smith, who led the team to six wins from their opening eight games this season, lost his starting spot after suffering a concussion in week nine against the St. Louis Rams.
Even though he had been in good form and quickly returned to health, coach Jim Harbaugh opted to stick with replacement Colin Kaepernick.
The rest is now part of 49ers history. Kaepernick has guided the team to their first Super Bowl in 18 years, where they will face the Baltimore Ravens, while Smith has sat and watched from the sidelines every Sunday.
Now, as the Super Bowl journey he began concludes without him, the only discussions in the media about Smith are where he will play once he has left the 49ers and how tough it must be for him to endure the hype for a game in which he will, injuries permitting, probably not throw a ball.
"I'm not going to lie about any of that. It has been tough at times for sure, tough to accept, tough to watch, but we're in the Super Bowl," Smith said.
"This has been an amazing experience. It's a great team, I love being a part of it. I have said it before, it's bittersweet a little bit, but still, it's been a great thing to be a part of."
Smith denied media reports that he had already asked the 49ers to release him from his contract.
"I don't know where this stuff comes from. I'm focused on this game and helping this team win a championship and doing whatever I can do. That stuff can wait. There is plenty of time for that in a week's time," he said.
Whenever the 49ers players and staff have been asked about Smith's involvement with the team, they have to a man praised the quarterback's professional approach to his job as back-up.
"Alex is a class guy. He's been through so much. He's been on an emotional roller coaster. I wasn't worried about Alex because I know that he can handle anything.
"He's been high, he's been low, and he's been through so much at a young age. So he can pretty much handle whatever comes his way," said tight end Vernon Smith.
Kaepernick himself confirms that Smith has been supportive throughout.
"Alex has been great. He has done everything he can to help me and help this team. To have a veteran quarterback like that on your side, making sure you're seeing the field well, is always great," he said.
In such a violent game though, Smith knows that an injury to Kaepernick means he could suddenly find himself with the ball in his hand at a vital stage of the Super Bowl.
"That's my job. Be ready to go," he said. "You never know, it's a crazy game, crazy things happen and my job is to be ready to go at a moment's notice."
