Can Someone Explain wtf happened in Mission Impossible?

I suck at understanding these movies, so someone tell me what was the twist in mission impossible? I just watched it again and i dont know who was on whose side or who was the bad guy or what. thanks

[Matt Williams]

I don't get why so many thought this movie was confusing. I thought it was pretty easy to follow and I get confused in movies a lot. Tom Cruise was set up and knew he was being set up but wanted to figure out if the chick was in love w/ him or not.

[splashpot]

Ethan knew Jim was the bad guy when he saw that inscription in the Bible. But he didn't know if Jim was working alone or if the girl was in on it too. So he tested her.

[cwsiggy]

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I suck at understanding these movies

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You would love the movie Primer. See it.