The best way to explain the motives of Ocelot is to explain his whole history and a little bit of the patriots. You might not know some connections so I'll parenthesis some things to help out
In Operation Snake Eater, Ocelot was a triple agent. He was originally posted by the Philosophers to work as a double agent under Colonel Volgins command in order to retrieve the Philosophers Legacy. He was then ordered under the CIA to help Naked Snake (Big Boss) under the code name ADAM. However a chinese spy pretending to be EVA (which is now known through the whole series as EVA and is known in MGS4 as Big Mama) showed up before Ocelot did, so Ocelot decides to help Snake out subtly without giving up his disguise. (Notice how many times he lets you get away and during the fight with volgin instead of shooting you he gives you ammo) Shortly after Snake eater, Ocelot recovers both halves of the Philosophers Legacy (one was in the american branch, the other KGB)
Around the 1970s using the Philosphers Legacy Ocelot, Eva (Big Mama), Donald Anderson (Sigint, The Darpa Chief), Zero, Clark (Para-Medic), and Big Boss form the Patriots. Well everyone in the Patriots views kind of shifted, and Big Boss breaks from the Patriots which leads to the Metal Gear games.
Also around this time Ocelot, leaves the patriots however unannounced that way he still has connections in and he can plan their fall from the inside. Also a little bit later Zero makes the "Patriots systems" which is kind of like....a self thinking computerized government. Ocelot goal is bent on destroying the program.
When Ocelot learned that a unit called Foxhound was coming in order under the lead of liquid snake he was more then happy to join and take part of to be close to one of Big Boss's sons. He joined in on the Shadow Moses incident. He also was working for Solidus Snake (George Sears, president at the time) Solidus main goal is to unveal the members of the patriots by setting off a hydrogen bomb in the middle of the new york to cause a break in the Patriot system defenses so he can reveal worldwide who the patriots where and hunt them down one by one. Ocelot still technically being one of them couldn't allow that to happen. So in MGS2 he stops Solidus however, a Virus was still upload into Arsenal Gear causing one of the patriot systems to break.
In MGS4 ocelot still hides under the guise of Liquid Ocelot, during the whole thing he manipulates everyone pretending to be part of the patriots. Naomi/Sunny create a virus that gets implanted and spreads to the remaining Patriot system. Drebin (who was recruited by the patriot system) injected the new version of Foxdie into snake to kill enemies of the patriots (which would be Ocelot) so at the end of the game, after all the fighting before he dies, Ocelot reveals they were pretty much on the same side and wanted one last fight with the closest thing he could get to Big Boss.
Pretty much, it is confusing yes, and I left a lot out, but it makes sense in a strange way. By the way i didn't edit this yet so if theirs some spelling or grammer thats like wtf, ill fix.
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CURRENTLY PLAYING: Warframe, Witcher 2
