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The reason Shepherd went rogue is because he lost 30,000 soldiers in that nuclear attack in Modern Warfare 1. If you remember the story mode someone on the Defense Cabinet says "we should have listened to you in the beginning, whatever you need you have a blank check."
He got tired of people ignoring him thinking he was an old paranoid man. He blew that CIA op's cover so that the russians would attack. Then has to make sure the intel from Makarov doesn't get in to the wrong hands so that his war machine gains momentum to take out the targets he feels are responsible for the first game.
That's my take on it anyways.
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