In 1995, Mulcahy made a Director’s Cut version known as Highlander II: The Renegade Version. The film was reconstructed largely from scratch, with certain scenes removed and others added back in, and the entire sequence of events changed. All references to the Immortals being aliens from another planet were eliminated; instead, this cut reveals that the Immortals are from an unspecified, distant past on Earth, banished by priests into random locations in the future to keep the Prize from being won in their lifetime (the option to return to the past is an option offered in addition to the mystical Prize and mortality of the first film). This version is generally considered a major improvement on the theatrical release, and obtained a far more favourable reception. Nevertheless, the events of both versions were generally ignored by the subsequent films and series.

The new version also removes a major continuity gaffe from the theatrical version, which had merged two separate swordfight between MacLeod and Katana into one longer climactic battle. The first sequence has MacLeod and Katana fighting in a large abandoned building about halfway through the movie (with MacLeod using a short sword), and the climactic swordfight takes place much later (with MacLeod using his original katana). Since the two sequences are merged, Connor’s sword changes for no apparent reason. The director’s cut version restores them to two separate battles, although it never shows how or when Connor reacquired his katana. The gaffe wherein Katana's sword changes from his giant "spring loaded" broadsword, to the smaller broadsword used by the two punks still exists in the final battle of both versions.

Still not completely satisfied, producers William Panzer and Peter Davis decided to revisit Highlander II once again in 2004. Dubbed the Special Edition, this cut was nearly identical to the Renegade Version, but with a few alterations. The most obvious change is the introduction of new CGI special effects throughout the film, including a now-blue shield as originally intended. Other significant changes include a small piece of voiceover work by Lambert and the inexplicable removal of a short scene near the end of the film in which Louise Marcus holds off a group of TSC guards with a gun. Shots of a crashed space ship where the Zeistian rebels meet in secret 500 years ago is altered so that it appears "A Very Long Time Ago" some rebels meet at an old stone fortress. However, modern looking firearms are still seen briefly in some of the desert battle sequences, as well as the use of explosives and gas masks.

The 'fairytale' ending Highlander II fairytale ending		A once lost alternate ending, commonly known as “The Fairytale Ending,” was shown only in some European theaters and has never been shown in any of the American cuts. The ending shows Connor magically returning to planet Zeist, taking Louise along with him, while Ramirez’ voice is heard in the background. An early version of this ending is shown on the Special Edition however it also includes footage of Virginia Madsen as Louise Marcus speaking to Christopher Lambert as Connor MacLeod. Madsen is on location while Lambert is suspended by wires in front of a blue screen. After a brief exchange where Connor asks Louise to come with him, the theatrical ending is shown where the two embrace in front of a field of stars, then transform into light streaks and fly off into space. This ending is sometimes seen in televised broadcasts of Highlander II: The Quickening. The VHS version simply cuts off after Connor looks up at the starry sky and smiles, after the smoke from the explosion of the December Installation clears.