Hours before Friday's deadline to make a decision, the team elected to exercise Aldon Smith's fifth-year option, preventing him from entering the free agent market next winter.
According to a report from the Bay Area News Group, Smith met with gerenal manager Trent Baalke Friday and Baalke informed the rest of the front office the meeting went well.
Smith has been one of the league's premier players at the position since coming into the league as the No. 7 overall pick in 2011. He's registered 42 sacks in 43 career regular season games.
The news comes a week after the Los Angeles District Attorney's Office announced an incident at Los Angeles International Airport when Smith allegedly made a false bomb threat was to be considered as a possible misdemeanor and not a felony.
Reports surfaced following the incident saying the 49ers were not likely to pick up Smith's option given his string of legal troubles. The talented outside linebacker missed five games in 2013 following an arrest for DUI when he left the team to attend a drug and alcohol treatment facility. He is also facing charges for illegal possession of assault weapons stemming from a party in the summer of 2012.
In addition, Smith had a DUI charges lowered to reckless driving from an incident in January 2012. The 49ers went 5-0 when Smith was away from the team last year.
"We're disappointed any time one of our players puts themselves in a bad situation," Baalke said last week prior to the team's local pro day. "You're dealing with some times in the year over 90 players. Most of the parts of the year...access of 60 to 70 players. There's going to be mistakes made. That's just a fact."
There's a Chance Smith could be facing further discipline by the NFL in the form of a suspension in 2014. With the 49ers agreeing to pick up his option, three things could happen to Smith in 2015: he could get cut and the 49ers wouldn't owe him any salary, he could make the team earning his $9.75 million salary, or he could make a different salary if he agrees to a contract extension in the meantime.
Had the 49ers not picked up the option, Smith would have been able to test the free-agent market next spring. The team could have franchised him for a number close to $12 million, over $2 million more than what he will make in 2015 after the team picked up the option.
The 2015 option is only guaranteed for an injury that would sideline Smith both 2014 and 2015.
With his $9.75 million salary, Smith will be the team's highest paid player in 2015. But that will likely change if and when Colin Kaepernick signs his lucrative contract extension. Kaepernick is in the final year of his rookie contract.
Kaepernick's representation has been in discussions with the team for a new deal that will reportedly average around $18 million per season.
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