- 50 minutes of fully produced but unreleased footage allegedly exists, including:
- Extended Wedding Sequence - Originally, Riker and Troi's wedding was much longer and featured Wesley Crusher (played by Wil Wheaton) in attendance. (He is still sitting next to Dr. Crusher in the theatrical version) Also during the wedding, Picard opens up to Lt. Commander Data and reveals his dismay over being a private loner all his life.
- The Seduction of Counselor Troi - In the original three-hour version, Shinzon's obsession with Troi runs much deeper and there are several scenes that show him seducing and tormenting her in her mind. A scene featured in the theatrical trailers show Troi struggling with the mind meld inflicted by Shinzon and his Viceroy. You still see the effects of the torturous mind meld in the theatrical version as Troi appears fatigued and psychologically drained.
- A scene of Data teaching his brother B-4 how to eat with a fork.
- Ambassador Worf and Dr. Crusher were also featured more prominently in the three-hour version and it was revealed that Worf was on his way back to Kronos after leaving Deep Space Nine and he was featured in more action sequences that were deleted from the theatrical release. Dr. Crusher is revealed to be considering leaving the Enterprise after receiving an offer from Starfleet Medical.
- Footage of Geordi and Data planning and executing the mission to rescue Picard on board the Scimitar was also deleted and featured the swapping places of Data and B-4.
- Extended ending - Riker and Troi board the USS Titan as he takes command as Captain and she resumes her job as ship's counselor. The instatement of a new First Officer on the Enterprise is shown. Picard bids farewell to Dr. Crusher as she accepts the offer from Starfleet Medical and leaves for San Francisco.
- Seven deleted scenes appear on the DVD edition with introduction by producer Rick Berman. In the intro, Rick Berman confirms that roughly 50 minutes of footage was trimmed from the original version. The seven deleted scenes make up about 17 minutes of this original footage and includes:
- A private conversation between Picard and Data over a glass of wine.
- Early introduction of Shinzon in the film (right after the wedding reception). This is the scene that includes the dialogue from the theatrical trailers, "But in darkness there is strength...(Viceroy)" and "The time we have dreamed of is at hand... the mighty Federation will fall before us...(Shinzon)."
- The second rape scene of Counselor Troi in a turbolift.
- A scene of Picard walking with Troi down a corridor and Troi explaining to him that he and Shinzon are two different people. This scene includes the line from the trailer, "It was like a part of me had been stolen...(Picard)."
- Sickbay getting ready for battle, a short dialogue between Dr. Crusher and Picard is shown.
- Worf warning Picard about the Romulans just before they leave for Romulus. This scene includes the dialogue from the trailer, "I recommend extreme caution...(Worf)."
- Original extended ending - A new First Officer is introduced on board the Enterprise and two funny moments are shown afterward. Instead of ending while the Enterprise is docked above Earth, this new ending shows the Enterprise flying away.
- In the version released in Singapore, the words "Star Trek" did not appear in the title screen or in the movie advertisements. The film was billed solely as "Nemesis".
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