John Woo's final cut of the film clocked in at 3-1/2 hours. The studio balked at this length and told him that the final length could not exceed 120 min. This could explain why there are so many plot holes and continuity errors in the theatrical cut.
The part of Mission Commander Swanbeck was originally offered to Ian McKellen. He was not able to accept the role, due to a prior theatre engagement in London and the part eventually went to Anthony Hopkins.
Luther Stickell's line "It's that simple, huh?" after hearing Ethan Hunt's explanation of what he thinks "Chimera" is was a joke about Mission: Impossible (1996), which was widely criticized for having an overly complicated plot.
SERIES TRADEMARK: At Hunt's meeting with Mission Commander Swanbeck, Hopkins offers him an espresso or cappuccino. At the preliminary meeting with Jim Phelps in Mission: Impossible (1996), Hunt asked if they could get a cappuccino machine.
The famous rock climbing sequence was filmed at Dead Horse Point in Utah. Tom Cruise was on cables which were then digitally removed. Ron Kauk was the climbing double and the overhang stunt was performed by main stunt double, Keith Campbell. John Woo was so scared each time but "Tom insisted on doing it".
The scene where Tom Cruise "peels off his face" to reveal Dougray Scott was achieved in one shot by shooting both actors against a green screen. Cruise, not wearing a mask, was simply told to place his hand in a pre-arranged position under his chin then pull his hand across his face. Scott wore a plain mask with sensors that could provide a computer with a three-dimensional view of his face. He then peeled off this mask to finish the scene. Cruise's face was superimposed on the mask as it is pulled away and the two images morphed together in the computer; the background of the 747 cabin was added in to replace the green screen. (Watch the scene with frame advance and you will see a slight transitional 'swirl' on the mask halfway through the scene). Kevin Yagher contributed some more traditional latex mask effects for other face-peeling scenes.
Picture editor Tony Ciccone was badly injured in a motorcycle accident on his way to work and was unable to finish the movie. It took almost a year of physical therapy for him to regain full use of his hands.
Oliver Stone was the first director attached to this film in the period after the first film's release. He reportedly wrote a treatment but backed out due to scheduling conflicts resulting from Tom Cruise's prolonged stint on Eyes Wide Shut (1999).
For the "knife-in-the-eye" scene, Tom Cruise insisted that a real knife be used, and that it stop exactly one quarter-inch from his eyeball, instead of somewhere vaguely near his eye, as John Woo suggested. The knife itself was connected to a cable that was measured carefully in order to achieve the effect and Cruise insisted that Dougray Scott use all his strength in the ensuing struggle.
The sunglasses that Tom Cruise wears at the climax of the climbing scene providing him with his mission brief are modified Oakley Romeos that are now discontinued. They were modified for their appearance in the film in three ways: the ear stems are different (the commercially available model had curved ear stems while the movie version has straight stems), the lenses used in the film aren't mirrored (to prevent the film crew being seen in the reflection) and the most obvious modification being the earpieces grafted on to the frames.
Was to be film editor Tony Ciccone's big break as a studio co-editor. Unfortunately, a motorcycle accident a year into production prevented him from finishing the film. He was given the lesser credit of additional editor.
A brief shot of children playing "Ring Around the Roses" is shown. This is a subtle reference to the plague that would ensue should the Chimera virus be released onto the world. According to popular belief, "Ring Around the Roses" was a kids' song based on the medieval Black Plague. In this theory, the "ring around the roses" represented a ring of people around a grave with roses on it. "Pocket full of posies" refers to people carrying flowers in their pockets during the plague, to combat the stench of the corpses in the streets. "Ashes, ashes" refers to the mass burnings of bodies. "We all fall down" refers to the multitudes of people dying. In fact, the rhyme dates from Victorian times, and originally did not contain these specific references, which were created in improvisational children's playing. Nevertheless, the legend connecting the song with the plague persists.