The Matrix ReloadedEdit
Early in the film, Bane was in attendance for a meeting within the Matrix between all of Zion's fleet captains. He helped to divert a group of Agents who interrupted the meeting and later was about to exit the Matrix when he was attacked by Smith, an Agent program that Neo had supposedly destroyed. Having transcended his original programming and evolved into a virus, Smith had become capable of imprinting himself on to anyone connected to the Matrix, whether they be programs, bluepills or redpills. Before Bane could exit, Smith attacked and assimilated him, turning Bane's Matrix avatar into another copy of himself. For all intents and purposes, this resulted in Bane's death as his mind had essentially been erased and Smith was now able to use Bane's corrupted avatar to exit the Matrix and take control of Bane's body in the real world.
Unfamiliar with the sensations of the material world, Smith - in Bane's body - attempted to adjust by purposefully harming himself, cutting his arms with a knife to feel the sensation of pain. He had always been disgusted by the nature of humanity and inhabiting a human body only intensified his hatred and fueled his new purpose of destroying them. While inhabiting Bane's body, Smith attempted to murder Neo in Zion, but was prevented from doing so as there were witnesses present. He would later board the Caduceus when it was deployed to initiate countermeasures against the Machines' invasion of Zion and took the opportunity to sabotage their efforts, prematurely firing the ship's EMP and disabling all of the nearby vessels, leaving them completely vulnerable as the Machines approached. Bane would survive this attack and would later be found unconscious by the Mjolnir.
The Matrix RevolutionsEdit
Bane would regain consciousness a few hours after being picked up by the Mjolnir. As the only survivor of the massacre at the defensive line, Captain Roland was interested in questioning him, believing that he may have sabotaged the Caduceus and fired the ship's EMP. His suspicions would prove to be correct, but he would realize too late. When Neo and Trinity took the Logos in order to fly to the Machine city of 01, Bane murdered the Caduceus' medic and boarded the Logos before it took off.Bane sabotaged the Logos by removing some engine fuses, disabling the ship's engines. When Trinity went to check the fuses, Bane ambushed her and tried to kill her. Trinity broke away from Bane long enough to call to Neo, but when Neo jumped down into the engine room he found Bane holding a scalpel to her throat. When Bane addressed Neo, he referred to him as "Mr. Anderson", something that only Smith had done before and so clued him in to the fact that Bane had been taken over by Smith.
Smith forced Neo to drop his lightning rifle and kick it to him, then threw Trinity into the fuse room and locked her inside. Once Trinity was out of the way, Smith held Neo at gunpoint, but Trinity pulled another fuse in the fuse room, knocking out the lights. As the lights went out, Neo lunged at Smith and the two struggled, causing Smith to fire the lightning rifle inside the room and causing damage. Smith gained the upper hand by grabbing an exposed power conduit and shoving it in Neo's face, cauterizing his eyes and blinding him. Smith hid in the darkness, wielding a steel pipe and taunting Neo. This was when Neo discovered that his new powers as The One allowed him to 'see' the golden auras of anything connected to the Source, the Machines' central mainframe. While he could no longer see Bane's body, he could see Smith's code inside it.
Just as the unwitting Smith lunged forward, Neo disarmed Smith and struck him in the head with his own pipe, killing him. This was seen in Neo's "Source vision" as Smith's head shattering and his body doing likewise when it fell to the deck. Smith was then disconnected from Bane's body, due to physical death.