Brooks benched in Smith's return

49ers outside linebacker Ahmad Brooks was mysteriously removed from Sunday's win over the New York Giants after Aldon Smith made his return from his nine-game suspension. The circumstances surrounding Brooks' benching remain dubious.

EAST RUTHERFORD, N.J. - Outside linebacker Ahmad Brooks, a week after forcing the game-clinching overtime fumble on Saints quarterback Drew Brees, did not play after the first quarter in Sunday’s win over the Giants.

The reasoning remains a mystery.

"We have something we're working through," Jim Harbaugh said after the game.

The 49ers said Brooks was not dealing with an injury. Once Aldon Smith made his 2014 debut in the second quarter after being reinstated from his nine-game suspension this week, Brooks' day was done despite leading the 49ers with four sacks on the year.

Brooks declined to offer specifics to reporters Sunday.

[Related: Bowman likely to return to practice this week]

Corey Lemonier played sparingly in Brooks' place in the rotation of outside linebackers after being benched in favor of rookie Aaron Lynch in Week 4's win over the Philadelphia Eagles. Lemonier came into Sunday playing a combed 12 snaps on defense since getting surpassed on the depth chart.

"Honestly, I don’t know what happened there," Lynch said of Brooks' benching. "I don’t know what the deal was. I love the guy. He’s a big brother to me. As far as what happened off the field or on the field, I don’t know what happened. We never talked about that. He was coaching me up and telling me what I needed to do. That’s it."

Around the Oct. 28 trading deadline, rumors surfaced the 49ers were shopping Brooks to the Cleveland Browns. He will count for roughly $9 million against the salary cap over the next three seasons.

Asked if Brooks' future with the 49ers is in doubt with Smith back in the fold, Harbaugh's words were pointed.

"We need Ahmad Brooks to win a championship," he said. "I feel that wholeheartedly, and I have felt that way."

Of course, Harbaugh's effusive praise hasn't been enough to keep players around before. Departed safeties Dashon Goldson and Donte Whitner, and receivers Jon Baldwin and A.J. Jenkins, have all been flowered during Harbaugh press briefings in the past.

Update: 6:40 p.m.

FOX Sport's Mike Garafolo is reporting Brooks took himself out of the game.

Per the report:

"A source told FOX Sports that Brooks was upset with the coaches' decision to take reps away from him and give them to Aldon Smith and Aaron Lynch during the team's 16-10 victory over the New York Giants. The source said Brooks told the coaches and his teammates he believed he should be playing every snap and didn't care to be part of a rotation, so he pulled himself from the game.

"Multiple media reports from MetLife Stadium stated Brooks wasn't standing on the sideline in an effort to get back in the game but was rather sitting on the bench, removing his cleats and getting the tape cut off his ankles."

To channel a cliche; a team can never have too many pass rushers. And with the way Lynch has been playing of late, a three-man rotation at outside linebacker could be a very dangerous card in the 49ers' hand during the stretch run and the playoffs, particularly against teams like the Saints, Packers, and Lions who rely so heavily on the passing game.

But it appears Brooks is on not board to be apart of a rotation with Smith and Lynch, who both played big roles in Sunday's win.

Next story:

49ers defense stands up in ugly win over the Giants

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