The body was that of a clone—Solidus.
Solidus had been created as the perfect clone of Big Boss. Unlike Solid and Liquid, who had been given various customizations, he was created to be exactly the same as Big Boss. Zero and the proxy AIs that rewrote the world for him were convinced that Solidus’s remains were those of Big Boss.
As for Big Boss, JD had implanted him with nanomachines and kept him in a state of eternal sleep. He was completely sealed away in both body and mind. Until the System was destroyed, he had been unable to wake. Ocelot and EVA wanted two things: to bring Big Boss back to life, and to end the Patriots.
EVA stole Big Boss’s body from the Patriots and reconstructed it by replacing the missing parts from Liquid, who had died at Shadow Moses, and Solidus. With the limbs and organs essentially sharing the identical genetic code, the transplants weren’t rejected by the immune response, as if they were happily returning to their former body.
But though Big Boss had been physically restored, his consciousness remained locked away. Then Ocelot, EVA, and Naomi put into motion a grand and complex scheme to free the world—and Big Boss—from their prisons.
First, Ocelot set about ceasing to be Ocelot.
His was a grotesque and woeful decision.
In order to revive Big Boss, Ocelot chose to sacrifice himself; to stop being Revolver Ocelot and become Liquid Snake. This was his ingenious ploy to deceive the System and hide his activities from the AIs.
Ocelot used nanomachines and psychotherapy to gradually transplant Liquid’s personality onto his own. Each day, he became less and less sure of who he was. Eventually, he lost himself. One might say that his fate was akin to death. With a smile on his face, he destroyed himself for Big Boss’s sake, believing, If giving up my insignificant personality will obliterate Zero’s repulsive world, the world I helped bring about, I will do so happily.
Into Ocelot’s vacant mind a fiction was planted. You are Liquid Snake, a clone born from Big Boss’s genes.
The psychodesigners overwrote Ocelot’s being with their version of Liquid Snake, created from a wide collection of bits and fragments; Gulf War reports on his interrogation by the AMN in Baghdad, the psychological test results from when he joined FOXHOUND, surveillance footage stolen from the Patriots, and, more than anything else, Ocelot’s personal impressions of Liquid from their time together in FOXHOUND.
From the Patriots, EVA had stolen the technique, a prototype of the system to control human will that was later completed in Manhattan under the S3 Project; the protocol Jack—as Raiden—had been the prototype of, using environment and role to alter the personality of a specific person. Through that ghastly technique, Ocelot became Liquid’s doppelgänger.
He became the son of that great warrior.
He had been born an ocelot but was now—even if only in fiction—a snake.
That might have been what he had always desired—to be the son of the warrior whom he respected more than anyone else.