The entire first movie is the mole hunt.A very elaborate one. Kittridge suspects Phelps from the beginning. Ethan is sent into uncover the mole. The murders of the team were not expected, but prepared for by having the second IMF team around in case something happened. The scene in the restaurant, the arrest of Ethan's parents, and the CIA invasion were staged to make Phelps think they were off his trail. Ethan was genuinely surprised by Claire at the beginning. The fact that she survived causes him to think she is in league with Jim, though he wants to not believe this. We see later that, as soon as he sees Jim and listens to him accuse Kittridge, he instead envisions Jim as the villain. He even suspects Claire for a moment. Kittridge does not seem surprised upon seeing Phelps alive, even though Ethan never said anything to prepare him for this.
Agent Brandt is gay"Next time, I get to seduce the rich guy."
Wistrom is the real mastermind in Ghost ProtocolWhy else would Hendricks be doing his assistant's job in Dubai?
John Voight's Jim Phelps is not the real Phelps.He's a rogue SYNDICATE agent that killed the real Jim (Peter Graves) and took his place. He decided that both the masquerade and his loyalty to the SYNDICATE are through, so he decides to be a mole for hire.
The Rabbit's Foot is the Luck Virus.The MI movies take place in the Red Dwarf universe. The Rabbit's Foot in MI:3 is a prototype Luck Virus. Untested. Dangerous stuff. Ethan Hunt is probably infected already. The virus may even be collected from the cells of top MI agents.
The real mole in the first episode was Dan BriggsBriggs saved the world more times in one year than James Bond does in a good decade, and how did the IMF repay him? They took his team away and gave it to Jim Phelps. What's more, his teammates never so much as spoke of him ever again. The first movie was his plot to destroy the IMF in general and Phelps in particular.