Here's the first actual chapter, be sure to read the prologue first. More comments at the bottom.

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One of the doctors on Shadow Moses Island was willing to perform the surgery, as long as he was allowed to leave the base and return to the continental United States after the procedure. Ocelot agreed, but soon after the surgery was finished he slipped a piece of C4 into the doctor's back pocket before he left. Needless to say, the doctor was in for a surprise once he left building.

With everything seemingly back to normal, Ocelot was talking to Liquid Snake in the torture room.
"It feels good to have my right hand back" Ocelot Said in joy.
"It's not exactly 'you're' hand, now is it?" Liquid replied.
"I suppose not, but it's definitely better than a stub!" Ocelot said defensively.
"Has it effected your marksmanship?" Liquid asked.
"Slightly, but I haven't broken it in yet." Ocelot replied.
"Any ideas regarding the launching crisis?" Liquid inquired.
"I'm afraid not. Maybe we should tell Raven and the oth-" Ocelot began to say.
"Hey, are you still there? Earth to Ocelot. Come in, Revolver" Liquid said jokingly. Ocelot's eye's began to look different. Ocelot began to speak again.
"ers... what... happ-" He began again until an unexpected voice was heard.

"What the hell is going on!?" Solid Snake's voice came from Ocelot's mouth.
"I should ask you the same thing, Ocelot." Liquid said, very confused.
"What are you talking about? I'm Solid Snake! You were just talking about us being brothers a few hours ago!" Snake said, equally confused.
"Oh, I see, you're just pulling my leg. You almost had me going at first, but come on. You channeling a dead guy through your hand? That's just ridiculous! (Hehehe) Still, that's a very convincing voice, how did you-" Liquid started rambling off before Snake interrupted.
"I'm only going to ask this one more time, what the hell is going on?" He called out. Just then a light bulb turned on in Liquid's head.
"Well, this is bar none the strangest thing that's ever happened. I'm not exactly thrilled that you're back, but I like a challenge, so I'll give you a chance to win." Liquid said.
"What?" Snake replied.
"I've already entered in the codes for the missiles, but I still won't launch them until Midnight. You have until then to stop the launch" Liquid said before running off, feeling a sense of accomplishment.

Snake ran to a corner of the room to look in a mirror, and was shocked to find that he was actually Revolver Ocelot. Or at least living in his body.
"I guess this means I can't use the codec anymore." Snake said before feeling a strange sensation in his body.
"Did I just black out for a seco... Where am I? Where's Liquid?" Ocelot said to himself. Snake took control again, and began thinking of what to do.
"Wait, the codec wasn't surgically attached to my ear or anything, I can just take it from my old body!" He quickly realized. Meanwhile, Liquid was glad to know that Snake was alive and his plot could continue as planned. Solid proceeded make his way through the compound, pretending to be Ocelot until he reached the point the had gotten to earlier before being captured.

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Completely original duologue all the way through this time. I kind of jumped to a late point in the game's story, (The one this parallels) but there's still plenty of stuf fixing to happen. Keep in mind this won't be to long, sice it's just a short story. I might do some longer stuff after this.