- In 1995 a "Special Edition" was released on video. It contains many new lines of dialogue, extended scenes of Tom Baker (from Shada), updated and vastly improved special effects, and a new Stereo Dolby Surround soundtrack.
- Among the changes made for the 1995 Special Edition included: A new opening scene showing the Tower, a number of scenes in different order (to reflect the original teleplay), several slightly extended scenes with additional dialogue, revised special effects (most notably the Time Scoop effect), and some revision to the footage used from Shada. The only major plot change resulting from these revisions is that, due to the use of different images from Shada to depict the Tom Baker Doctor being trapped in the vortex, Romana is no longer depicted as also being trapped (which reflects the actual teleplay which makes no reference to her).
- Yet another Version was aired in Germany in 1995: This Version was split into 3 Parts, each having variable running times, cutting many scenes to trim the overall running time down to roughly 77 Minutes and exclude scenes with Liz Shaw or the Battle between the Cybermen and the Raston Warrior Robot upon others.
- The original video release in the 1980s had some minor cuts from the original TV broadcast. These bits were restored for the Special Edition release.
- The unfinished six-part episode "Shada," from which Tom Baker's scenes were lifted for this film, was later completed and released to video as Doctor Who: Shada (1992) (V). This release includes the original version of the footage used for Five Doctors.
- Another version was the same as 90-minute story, but cut into four 25-minute episodes for the series' syndication package. The three extra sets of opening and closing credits and reprised "cliffhanger" footage account for the different total running times.
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