Your journey begins in the deserts of Afghanistan, where you've been transported by a group of mysterious individuals. Your goal is to rebuild your military and uncover the truth about your past. You're armed with a prosthetic arm, a souvenir from your time in a Soviet gulag, and a burning desire for revenge.

As you regain your strength, you're approached by a woman named Quiet, a skilled sniper and your future ally. She informs you that you've been in a coma for nine years and that the world has changed dramatically. Your former ally, Big Boss, has been presumed dead, and his legacy has been all but forgotten.

Your story begins in a hospital, where you awaken from a nine-year coma. You're suffering from amnesia, and your memories are shrouded in mystery. A mysterious organization known as Cypher, led by a charismatic and cunning individual known as Liquid Ocelot, has been manipulating events from behind the scenes.