Sometime after the Big Shell Incident, Ocelot had Liquid's arm removed from his body and replaced with a fully cybernetic arm. Ocelot believed that the arm was driving him insane in the presence of Solid Snake.
Ocelot later transformed into a Liquid Snake doppelganger, in order to achieve his plans against the Patriots. In order to trick the Patriots to believing that Liquid had control of Ocelot, he volunteered himself to undergo gene and hypno therapy to make himself believe that he was in fact Liquid Snake.
After EVA was able to enlist Raiden to retrieve the body of Big Boss and replace it with Solidus Snake's body, who was a perfect clone and thereby identical, Ocelot would be able carry out his part of the plan and use Old Snake to destroy the Patriots and thereby awaken Big Boss who then could find and kill Zero. The missing pieces of Big Boss' body were rebuilt from organs from Solidus and Liquid, and his full healing process began to take place.
