Bane was a member of the crew aboard the rebel human ship Caduceus, who stayed behind inside the Matrix with Malachi in order to contact the Oracle, only to have a fateful encounter with the clones of Agent Smith. Malachi escaped, but Bane is "taken" by Smith and made into another clone. As a result, when Bane left the Matrix, although he was physically still himself, his mind was irreparably altered, "infected" by Smith's consciousness. Bane-Smith attempted to kill Neo in Zion, but failed and, remarkably, no one caught onto the fact that he wasn't himself.
Later, Bane-Smith tried to volunteer the Caduceus to be one of the ships to find the Nebuchadnezzar, but Ballard refused to allow it and so Bane-Smith decided to foil the the counterattack against the Sentinels instead. He killed the Caduceus' crew and activated the EMP prematurely, putting all the other ships out of comission, allowing the Sentinels to slaughter their crews. Bane-Smith was later picked up by the Mjolnir, the sole survivor of the battle. He claimed ignorance, saying that he did not recall anything, but dropped the facde after realizing the others were already suspicious.
He killed Maggie and then snuck aboard the Logos to confront Neo and Trinity, and he and Neo fought for control of a plasma rifle, damaging much of the ship in the process (not to mention Neo's eyes). Thinking Neo was blind, Bane-Smith swung a pole at him. Able to see via his connection with the Source, Neo ducked and then killed Bane-Smith by decapitating him.