As Eli emerged from the cockpit he was approached by a squadron of XOF soldiers ready to kill him. He also explained that he knew of Zero's plans and the Boss' wishes, and passionately revealed his plans; worldwide ethnic cleansing with the parasites, both his hatred for Zero and his broken childhood where he was heartlessly stripped of his culture, quoting the Romanian philosopher The XOF transport parked at the Serak Power Plant, the lair of the dormant Sahelanthropus, which was almost ready for activation. Venom Snake attempted to kill Solid Snake before he could escape the doomed Outer Heaven but failed.

Miller later informed Snake that Mosquito was a former member of the Militaires Sans Frontières, and that he had survived the attack on Mother Base. Sometime later, the Diamond Dogs pilot who was forced to fly the child soldiers off of Mother Base with Eli was finally recovered about fifty miles inland to Africa from the Seychelles waters. Venom Snake wasn't sure whether he liked DD or not, as they were both trying to figure each other out. Ocelot first met Venom Snake outside the hospital and saved him. He says the two have created "legends" and the Venom Snake is considered a "friend" as he now holds he title in Diamond Dogs. When Zero visited the comatose Big Boss in Cyprus, he acknowledged Venom Snake's existence, but saw him as little more than a tool to protect the real Big Boss whom he valued so much more. Miller vowed that Skull Face would pay for the epidemic. Knowing that they didn't have much time, Big Boss, disguising his face and calling himself "Ishmael," helped Venom Snake escape from the hospital in the midst of an attack by XOF.

Unlike Heroism, no Demon Points are awarded or removed for completion of objectives. He refers to Big Boss as Ahab, a reference to Captain Ahab in the same novel. In the ensuing confusion, the XOF forces pulled away Skull Face from the area, as Sahelanthropus gave chase towards Snake. Snake interrogated Skull Face on the whereabouts of the third English vocal cord parasite vial, to which Skull Face replied that it was "Venom Snake and Miller preparing to exact revenge on Skull Face for his role in Mother Base's destruction.Needing to tie up loose ends in the aftermath of Skull Face's death, Snake commenced missions such as recovering a dead informants information on Skull Face's plans, rescuing a Still curious about Huey's dealings in MSF's destruction, Snake infiltrated the Soviet Central Base Camp in Afghanistan a second time and found the Immediately after this, Ocelot informed Snake that Soviet personnel had retrieved the dormant body of the Man on Fire and placed it at the Yakho Oboo Supply Outpost. Snake was given a mission to destroy the CFA's Walker Gears, and around the same time Huey developed a personal walker for Snake's own use: D-Walker. Suddenly, Sahelanthropus burst into the hanger, being controlled by Tretij Rebenok, who Snake tried to shoot in vain. Kojima and the player creating the story together "is something traditional movies and books could not do. Snake would later embark on various missions to capture and recruit wandering soldiers that hailed from the original MSF Mother Base. However, Quiet was no where to be found. However, as time went on distance increased between the two, with events such as the sparing of both Quiet and Huey's lives broadening the gap, yet, Miller continued to support Venom Snake. Both being at least somewhat laconic, the two understood each other very deeply and silently respected one another's skill on the battlefield. He was soon given command over the mercenary unit Diamond Dogs, which had been founded by Venom Snake went on to command the military fortress Morpho, Miller, Big Boss and Venom Snake posing for a group photo on the original Mother Base, on December 5, 1974.The helicopter arrived back at Mother Base just as it was being attacked by Cipher's strike force XOF. He also lacked Big Boss' outspoken enthusiasm for firearms or food.