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The movie kicks off with an IMF agent running on a roof, shooting back at people. He jumps off and lands on a inflatable and somehow doesn't stick around to jump on it. He spots his target but it's too late - she shoots him first. Tough break.

Cut to Ethan Hunt. He's in a Moscow prison. Suddenly, Dean Martin begins to play over the loud speaker and his cell is unlocked. It's all Benji. He's outside in a truck watching on the camera. For some reason, Ethan doesn't go through the next open door. Instead, he goes to free someone and take him with him and Benji and very confused. But it works. They get to the room, the floor explodes and they escape. 

Ethan knew that dude was his informer would be tortured and killed, so he rescued him and granted him his freedom. Jane is new and she tells Ethan that guy at the beginning of the movie was Agent Hanaway and he was killed while intercepting a routine courier drop. The courier was carrying Russian nuclear launch codes & these were now in the hands of the assassin that killed him.

Hunt knows that IMF has been looking for an extremist, code name Cobalt. Cobalt is known to have a nuclear device and with the theft of the launch codes, his identity is now top priority for the IMF.  Cobalt was a nuclear strategist for Russian intelligence. So Ethan has to go to Russia to break into the secret Kremlin archives and locate files identifying Cobalt. Easy right? Well apparently Cobalt is already on his way to the Kremlin, which gives Ethan 5 hours to complete his mission.

This mission is going great but when he gets to the archives, he finds out that what he needs is already missing. Then someone taps into the IMF frequency and their cover is blown. So Ethan aborts the mission. Suddenly, a bomb destroys the Kremlin which knocks Ethan out and he awkes up in a Russian hospital. He finds out that he is now a wanted man, so he has to escape. 

The IMF picks Ethan up and catch him up to speed but their vehicle is attacked. One dude dies but another dude named William Brandt survives with Ethan. He finds out that the Russians have called the attack an undeclared act of war and the US president activates "Ghost Protocol",  which disavows the entire IMF. 

Based on Ethan's description of who he saw in the Kremlin with a briefcase, they identifies Cobalt as Kurt Hendricks. They believe Hendricks bombed the Kremlin and got the Russian nuclear launch-control device, and now needs its codes from the Dubai.

So off to Dubai they go! Ethan has to hack the server room. Obviously the only way to do that is from the outside with him using these special gloves hundreds of stories in the air. 

The plan is to make Wistrom, who is there on Hendricks behalf, believe he is getting the real codes, which are actually from Ethan and Brandt who are with the actual real codes in another room acting like they're the buyers. It's a whole thing. The plan is going great until the code women realizes that Brandt is taking pictures with his eyes. Wistom is getting away, so Ethan chases him into a sand storm. Turns out, Wistom is just Hendricks in a mask and he gets away! This is bad news. 

The team is all mad at each other. Hendricks got away and Jane accidentally kicked the seller out of a window. Whoops. It's at this point that Ethan accuses Brandt of keeping secrets from them because his fighting skills show that he's not just an analyst. Brandt admits he used to be an agent on the field. He was actually security detail to Ethan and his wife Julia. Julia was killed by a Serbian hit squad, prompting Ethan to pursue and kill them before he was caught by the Russians and sent to prison, where he was at the beginning of the movie. Brandt blames himself and never wanted to be out on the field again. 

They get word on where Henricks is going to be next. So off to Mumbai they go. They go to a party being thrown by Indian telecommunications guru. They believe he has struck a deal with Henricks and that he's going to use his sattelite. So Brandt breaks into the server room to take the satellite offline while Jane gets hot shot tech guy to reveal the satellite override code. 

But Hendricks takes the servers offline before they can finish the plan. 

He fires a nuclear missile on San Francisco from a Russian submarine which would look like retaliation for the Kremlim bombing. The only way to stop the missile is via the abort sequence on the launch device that Hendricks is carrying. Hunt pursues Hendricks and the launch device while the other team-members attempt to bring the broadcast station back online so that the abort command will transmit.

Hunt and Hendricks fight over the launch-control and he's able to hit the button and the power turns back on with 1 second to spare. No Nuclear war today! Plus, the IMF is proved innocent. 

The team comes together to celebrate and he gives them all a new mission. Brandt refuses at first until Ethan explains that Julia isn't actually dead, it was all a cover, so he doesn't have to worry about it. Off to the next mission they go.