Ahhhhhhhhh I found it. My bad guys I made a mistake.
An unknown period of time after his rescue from Afghanistan, Miller eventually discovered Venom Snake's identity as a phantom of Big Boss, meant to act as a decoy on the world stage. He confronted Ocelot with this knowledge, and Ocelot decided to let him in on Big Boss' true plan of creating Outer Heaven, an army that was a nation onto itself, and asked Miller to aid Big Boss in his coming revolution by continuing to work alongside him and support Venom Snake in growing Big Boss' legend. Miller, however, refused to have any part in said revolution; he felt utterly betrayed by this revelation and gave up on his former friend, declaring that while he would continue to play his role as Venom Snake's business partner for now, but only in order to make Big Boss' phantom and
son stronger in order to one day send him to Hell. Ocelot coolly warned him that if he really decided to go against him and Big Boss and switch back to Cipher's side, then the two of them would be enemies and he would oppose him by aiding
the other son. Miller grimly accepted this and told Ocelot that he would be ready when that time came, but for now it would be in both their best interests to just learn to coexist.
Miller would indeed continue to keeping up appearances for a while, but he eventually broke with Diamond Dogs, seeking the employ of official governments once more.
So Miller didn't know at first, felt betrayed when he learned the truth, and decided to turn his back on Big Boss after he lied and tricked him and expected Miller to just go along with it.