Hunt is seen as the main suspect as he learns that the mission was a set-up to expose a mole who had been selling secrets to an arms dealer called Max (Vanessa Redgrave); the real files are still secure at CIA headquarters in Langley.

He recruits a team of other disavowed agents such as hacker Luther Stickell (Ving Rhames), pilot Franz Krieger (Jean Reno), and Jim's wife Claire (Emmanuelle Béart), the only other survivor of the mission in Prague, to help him break into CIA headquarters in order to steal the genuine list in exchange for an introduction to the real mole, which he successfully does.

He is forced to once again go rogue in an attempt to track down the sadistic arms dealer, Owen Davian (Philip Seymour Hoffman) and secure a dangerous mystery item known as the 'Rabbit's Foot'.

With the help of his IMF team: Stickell, Declan Gormley (Jonathan Rhys Meyers), and Zhen Lei (Maggie Q), Hunt finds the Rabbit's foot, saves his wife, and kills Owen Davian in Shanghai.

It is also revealed that Hunt had Julia's death faked to protect her, something only he and the IMF Secretary knew about, giving him the pretext to infiltrate the prison his team freed him from in the opening scene.

In the fifth film, Hunt is assigned a mission that culminates in him hanging outside of an A400M military aircraft 5,000 feet above the ground in Belarus to recover a package that contains VX nerve gas.

Although this mission succeeds, when he learns that the thieves responsible for stealing the gas lacked the connections to do so, Hunt begins to uncover evidence of the existence of the Syndicate, a consortium of covert operatives who wreak terrorist attacks worldwide.

Eventually, he and his former team (Benji Dunn, William Brandt, and Luther Stickell) along with MI-6 agent Ilsa Faust (Rebecca Ferguson) learn that the Syndicate was actually originally a British project to perform missions without oversight, but British agent Solomon Lane (Sean Harris) took the plans and went rogue, now seeking to steal files that would grant him access to various established bank accounts to finance future Syndicate operations.

In the sixth film, an IMF mission goes wrong when Ethan chooses to save Luther after the latter is taken hostage, allowing a splinter group of the Syndicate, known as the Apostles, to gain access to three plutonium cores that could be used to create nuclear weapons.