Franz Krieger: If we're going to Virginia why don't we drop by Fort Knox? I could fly a helicopter through the lobby and set it down right inside the vault. And it would be a hell of a lot easier than breaking into the goddamn CIA.
Ethan Hunt: I thought I was going to see Max.
Matthias: You misunderstood. No one sees Max.
Ethan Hunt: Then what am I doing here?
Matthias: Allowing Max to see you and hear what you've got to say.
Ethan Hunt: I don't communicate very well through a shroud.
Matthias: If Max doesn't like what you have to say, you will be wearing that shroud indefinitely.
Ethan Hunt: Can I ask you something, Kittridge? If you're dealing with a man who has crushed, shot, stabbed, and detonated five members of his own IMF team, how devastated do you think you're gonna make him by hauling Mom and Uncle Donald down to the county courthouse?
Jim Phelps: We're being ambushed Ethan. Abort! That's an order.
Ethan Hunt: Negative. Golitsyn is on the move.
Jim Phelps: No, dammit, I said abort.
Ethan Hunt: Eye on the package. Jim, I'm Coming.
Jim Phelps: Of course he knew. Just when he knew is something of a mystery. You mind telling me, Ethan? Was it before or after I showed up in London?
Ethan Hunt: Before London. But after you took the Bible from the Drake Hotel in Chicago.
Jim Phelps: They stamped it, didn't they? Those damn Gideons.
Franz Krieger: Try any sleight of hand with my money and I'll cut your throat.
Senator John Waltzer: We were living in a democracy the last time I checked.
Answer: Ethan never thought it was a mole hunt to trap Jim. He found out from Kittridge at the restaurant that it was a mole hunt, but Kittridge believes that Ethan is the mole (the money his parents mysteriously receive). At the station Ethan realises that Jim must be the mole since it is too convenient both he and his wife survived. However, the hunt to catch the mole was never directed at Jim - Kittridge never suspected him until at the end when he sees Jim alive.
swordfish
Actually had suspicions before Jim showed up. Ethan found the Bible that was stamped from the Drake Hotel. Where Jim had literally just come back from before the mission. It made no sense otherwise why that would be in Jim's possession.