The 49ers’ fears of a season-ending injury for linebacker Kwon Alexander were confirmed Friday when the team announced he suffered a torn pectoral vs. the Cardinals on Thursday Night Football. Alexander was an essential piece in the heart of the 49ers’ front seven, and replacing him won’t be an easy task for San Francisco.
We’ve twice seem them struggle when he’s been out of games. It happened Week 1 when he was ejected for a helmet-to-helmet hit on Buccaneers quarterback Jameis Winston, and it happened again Thursday night.
Alexander isn’t necessarily the best player on the 49ers’ defense, but his importance cannot be understated. Replacing him won’t be easy, but the 49ers have a few options in the facility already, making a free agent signing unlikely.
Here’s what the 49ers’ depth at the now-vacated Will linebacker spot looks like:
Dre Greenlaw

The rookie fifth-round pick is the first option for San Francisco. He earned the starting Sam linebacker job out of training camp, and head coach Kyle Shanahan said Greenlaw would slide over to fill Alexander’s place.
The roles of the Sam (strong side) and Will (weak side) linebackers are different, but they require largely the same skill set. The Sam is on the field much less often than the Will since the Sam leaves the game in sub packages. Alexander was so effective in that spot because of his athleticism and coverage on underneath routes.
Greenlaw is a superb athlete as well, but it’s not easy as stepping in and being a good athlete. He’ll have to play heads up, aggressive football and be a sure tackler to continue giving San Francisco effective play out of the position next to Mike linebacker Fred Warner.
The rookie out of Arkansas played 56 snaps in that Week 1 win following Alexander’s ejection. He’s yet to eclipse 30 since then, but he’ll be on the field for essentially every down moving forward. This is a huge test for the first-year pro stepping into a starting role.
Azeez Al-Shaair

Al-Shaair was an undrafted rookie in camp, and was somewhat of a surprise selection for the final roster after suffering a bad knee injury his final year of college at Florida Atlantic. He was a monster before the injury in college, and carved out a roster spot mainly as a special teams player. His role will expand though per Shanahan. Al-Shaair will likely step into the role Greenlaw is leaving to take over for Alexander. That’ll mean limited, but important snaps at the Sam linebacker spot.
In his rookie campaign, Al-Shaair has played just 33 defensive snaps, including 29 combined in two blowouts over Cincinnati and Carolina. He’s posted just one tackle this season.
It’s unlikely Al-Shaair pushes Greenlaw for the starting job on the weak side, but he’ll see an uptick in playing time as the depth at linebacker thins out.
Elijah Lee

Lee played a lot for the 49ers last season, but couldn’t make the final roster over Greenlaw and Al-Shaair. The three-year veteran started five games for San Francisco a year ago, and racked up 65 tackles with three tackles for loss.
He’s been on the practice squad this season, and is the logical choice to elevate to the active roster once Alexander goes on IR. Shanahan mentioned Lee as a player who would be ‘next man up’ in the linebacking corps.
Like Al-Shaair, Lee isn’t liable to jump up to scoop a starting spot, but he’d provide immediate depth and familiarity with the 49ers’ defensive scheme. Lee was a productive player when called upon a season ago, but the fact he couldn’t beat out a fifth-round pick and undrafted rookie for a roster spot isn’t a great sign for his future playing time. He’ll likely see time on special teams if he is given a roster spot.
On the other hand, if the 49ers feel like they need more experience in the middle of the defense at some point, Lee gives them an option to plug in with NFL starting experience.