Smith has been at the center of many controversies during his tenure in San Francisco, and before being benched for second-year quarterback Colin Kaepernick, he had always found a way to regain his starting job.
It looks to be impossible for that to happen once more.
A shoulder injury forced Smith to miss most of 2007 and all of 2008 and stained the relationship Smith had with then-head coach Mike Nolan. In 2010, Smith again seemed ready for a change of scenery following the Mike Singletary era, but when the 49ers signed Jim Harbaugh as their head coach, Smith was inclined to return on a one-year contract.
In 2011, Smith enjoyed his best season at the NFL level, throwing for over 3,000 yards and 17 touchdown passes with a quarterback rating of 90.7. His signature game came in the playoffs, when he masterminded a tremendous comeback at home against Drew Brees and the favored New Orleans Saints.
In some ways, Smith's quarterback controversy under Harbaugh first started the following offseason, when Harbaugh took interest in Peyton Manning. Whether or not Manning, who eventually signed with the Denver Broncos, ever would have signed with San Francisco is unknown, but the fact that Harbaugh showed at least some interest in the future Hall of Fame quarterback gave many the impression that Smith's days as a 49er were numbered.
Despite the issue, Smith signed a three-year deal with San Francisco; a contract laden with options allowing the 49ers to back out each year. Even though the contract's terms hinted that the 49ers may be interested in ending their relationship with Smith at any time, Alex seemed poised to help guide the team towards the playoffs again in 2012.
Then came his concussion on November 11th against the St. Louis Rams.
Before that point, Smith seemed poised for another solid year to back up his efforts in 2011. His completion rate was the highest in his career and his quarterback rating was 104.1, certainly statistics that would make a substitution at the position hard to justify.
When Kaepernick took over, and then started again the following week against the Chicago Bears, Smith had to assume that he would again start once he had been cleared to play.
Harbaugh felt differently.
It is hard to argue with Harbaugh's decision. Kaeperick's raw talent, highlighted by his stronger arm as well as his rushing abilities, is superior to that of Smith. Those talents helped the 49ers beat the Saints on the road in Week 12 following the Bears win. The one factor in question was whether or not Kaepernick's experience, or lack thereof, would be a factor.
Kaepernick has shown, however, that he has what it takes to learn from each game. Veteran tight end Delanie Walker told 49ers.com, "He’s getting comfortable week-by-week and he’s just going to keep getting comfortable as the season goes.”
Should the 49ers try and retain Alex Smith in 2013?
For Smith, Kaepernick's confidence and abilities may very well mean the end of an era.
Smith publicly stated that he was upset at having lost his job because of a concussion. Having felt that he did nothing else that justified him losing his job, Smith even hinted at his own uncertainty with the team. "I have no idea what's going to happen from here. All I can do now is just prepare and get ready," Smith told the Associated Press (via CBS St. Louis).
A change of scenery may very well be the best thing for Alex Smith. All signs point to Kaepernick as being the future of the 49ers. Smith unquestionably wants to start and there are plenty of teams looking for quarterback help.
For the 49ers, holding on to Smith as a backup makes little sense. He is set to make at least $7.5 million in 2013 plus incentives. That is a pretty expensive backup. Trading Alex Smith is also a plausible scenario, but given the nature of his contract, the 49ers may be better off simply cutting him. If the 49ers were able to do that before the April 1st deadline, they would owe only $1 million of his base salary (per Niners Nation).
Of course, San Francisco could try and trade him, but if there is little or no market for Smith, the 49ers would be losing another million in dead money.
San Francisco would love to spend the money saved on letting Smith go to sign one or more of its current starting players to an extension. Safety Dashon Goldson may be the benefactor here.
Regardless of the details, the 49ers have made a statement about where they want to go from this point. Kaepernick is their quarterback of the future and Smith shall be shown the door at the end of the season.
For Smith, it is an opportunity to put a controversial and difficult phase of his career behind him and move forward. He's probably felt this way before, but this time, it is for real.
It is a dirty business, but such is football.