Ethan and Benji follow Ilsa to Morocco, where they break into a secure facility to retrieve encrypted data about The Syndicate. Ethan must hold his breath for 3 minutes as he enters a submerged cooling facility to override a security system allowing Benji to download the contents to a flash drive.
Ethan is a little clumsy underwater, and Ilsa needs to bail him out - rescuing Ethan, and later giving him mouth to mouth. She soon tasers Benji and makes off with the flash drive. IMF give chase, and help defeat Syndicate bikers on her tail, but she gets away.
Ilsa meets with British Intelligence to give her handler, Attlee, the flash drive. But Attlee wants her to keep on with her assignment getting close to Lane, even if it means her death. She returns to Lane, who finds that the flash drive was wiped.
Ilsa reaches out to Hunt, knowing that Benji made a copy, and when they all meet Lane's men abduct Benji. Benji is used as a bargaining chip to force Hunt to get the voice and biometrics of the British Prime Minister to unlock the drive.
IMF let Hunley (Alec Baldwin) know their position, and at a function for the Prime Minister they summon him to a side room. It's soon obvious that Attlee is the one behind The Syndicate, but before he can defend himself he shoots a truth-dart into the PM's chest - and takes off his mask to reveal the face of Ethan. The real Attlee enters the room, and is tasered/'darted' too. Hunley agrees to go with the plan, and they unlock the drive.
Before they can retrieve Benji, Ethan memorizes several transactions of the drive, and then wipes it.
Benji is wired to a bomb, to explode in 3 minutes. Ilsa has instructions to shoot both of them after 3 minutes as well. Ethan negotiates with Lane, and offers him one of the account numbers. Lane stops the timer, and Benji is allowed to leave. As the Syndicate agents move in, Ilsa and Ethan shoot their way out and make a run for it.
Ilsa faces off against the Bone Doctor in a knife fight, and wins. Ethan is hurt, and chased by Lane. He crashes through a window, and down a shaft. Lane jumps down to finish him off - but finds himself trapped in a glass cage. They turn on the nerve gas, and IMF pack him in a van.
Later at the congressional hearing, Hunley turns around his plan to dissolve IMF and claims it was all part of an elaborate secret plan. As he leaves with Brandt, it seems he's in pole position to be the next Secretary of State.