Their return to Mother Base occurred in the middle of an attack by XOF forces. Miller and Big Boss provided support and covering fire for MSF soldiers attempting to evacuate the base via chopper, narrowly escaping before the strut collaPSed. After telling Big Boss that the inspection was actually a smokescreen, Kaz tried to interrogate Paz irritably, only to be restrained. Big Boss eventually witnessed Paz's death when she exploded after jumping out, learning that she had in fact been implanted with two bombs rather than one as earlier believed. The explosion sent the MSF chopper into a collision course with a pursuing XOF chopper.
Later, Big Boss, Miller, and a third individual were treated in a hospital emergency room, where Big Boss would seemingly fall into a coma due to injuries sustained from Paz's bomb going off. In actuality, his coma was faked, and he went into hiding at the behest of Miller, Ocelot and even Zero, the latter of whom gave the idea to hide them at the British Air Force hospital in Cyprus. In order to ensure he hid well, Big Boss proceeded to give a new identity as Ishmael, even foregoing the eyepatch and removing his defective eye by replacing it with a glass eye while disguised as a common prisoner. They also had the medic dolled up to resemble Big Boss via facial surgery, both to distract those who want Big Boss dead and to keep the legend alive. He then spent nine years watching the medic, now named Venom Snake, while he is in a coma. In addition, he also had Miller and Ocelot deliberately act as if he actually were Big Boss to ensure the plan went off without a hitch
True to the plan, Venom Snake, given the name Ahab, acted as the lightning rod, with the various soldiers focusing on Venom Snake while otherwise ignoring for the most part Ishmael. Big Boss then proceeded to save Venom Snake from a female assassin by setting her alight after she was sprayed with rubbing alcohol, forcing her to flee through a window. He then led his counterpart through the hospital, also showing him the motions in a subtle manner. He then ended up knocked out during the escape after commandeering an Ambulance due to gunfire from a gunship, although after the crash, he escaped, leaving no trace of himself behind.