Ocelot's interrogations, Huey's explanations were riddled with holes, excuses, and contradictions. Ocelot also supervised Quiet's torture for an explanation after learning that she was a carrier for the vocal cord parasites, although he disagreed with Miller's belief that she was a threat. He believed that Quiet is truly loyal to Venom, having fallen "in love with the legend", the same as when he was younger. Snake ultimately sided with Ocelot, demanding that Miller let her go.[12]

After finally locating their whereabouts, Ocelot took part in the mission to take down Eli and his "Kingdom of the Files", to recover Sahelanthropus and neutralize Eli, infected by a stolen vial of English-language parasites, before could spread the infection any further. In the aftermath, Venom Snake planned to evacuate Eli for medicaltreatment, but Ocelot convinced him to leave him behind, pointing out that his infection was becoming dangerously contagious. They ordered Diamond Dogs to bomb the island with napalm to make sure any remaining trace of the parasites might be destroyed.

Ocelot eventually recovered his suppressed memories, and some time later, Miller discovered the truth for himself and confronted him. Ocelot explained Big Boss' true plan of organizing the nation of Outer Heaven, and asked Miller to aid the revolution by continuing to support him and Venom Snake. Miller, however, feeling betrayed and refused to take part. He instead declared that while he would keep up appearances in front of Venom Snake for now, he would only do so to undermine Big Boss by strengthening his phantom; one day, he