The original version of the movie contained several scenes that were cut before release:
- an extended library scene in which Riker and Troi throw small paperballs at each other. This scene also include some lines by the Librarian (Lee Arone-Biggs) and a Trill Officer (Max Grodénchik);
- a scene in which Picard and Anij kiss each other;
- a scene in which Picard spills cheese on a PADD displaying the Briar Patch;
- the actual ejection of the warp core;
- Data punching some Son'as on the planet and nailing them with iso-linear tags;
- "The will be no cover-up!" line on the Son'a ship.
The original version of the fight between Picard and Ru'afo contained an additional scene. After Picard was beamed away by the Enterprise, Ru'afo fell into the planet's rings and was regressed into a young child. This scene was cut from the final film, but a "Young Ru'afo" is still listed in the credits.
In the Australian television release, the close up of Admiral Dougherty's face being stretched until he dies was shortened.
Early previews featured a cameo appearance by Quark, the barkeeper from Star Trek: Deep Space Nine (1993). This scene was cut because director Jonathan Frakes thought it didn't work well for the film.