Mission Impossible (film)/WMG

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 Protocol
Why else would Hendricks be doing his assisntant'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.