Scriptwriter Keiko Nobumoto originally wrote Macross Plus as a feature-length work before the script evolved into a four-episode OVA. Macross Plus Movie Edition returns is closer to the story that was initially planned feature length. It compiles of most of the footage from the original OVA, along with approximately 20 minutes of some new and/or alternative footage. An alternate climactic fight between Guld Goa Bowman and an unmanned drone fighter was the highlight of the new footage.
A subtitle-only version of Macross Plus Movie Edition was released on VHS in the U.S. through Manga Entertainment, with a DVD release in 2000. The DVD version is a direct transfer from the VHS release, causing the subtitles to be part of the footage itself, so they can't be turned off. There is no English dub for the movie version.
A subsequent remastered blu-ray editions was released, but could not be sold in the States due to a legal situation enacted by Harmony Gold. A new re-release is expected in 2016, featuring new cover artwork by Koji Morimoto.
- The opening of the movie shows Isamu already testing the YF-19 (an extended version of his first test flight of the YF-19 from Episode 2) and meeting Guld for the first time in the hangar afterwards, as opposed to just arriving at Planet Eden and meeting Guld at the meeting between the two design teams.
- In that same scene, Isamu invites Lucy Macmillan on their first date. This is an alternate version to which he crashed a flight simulator in Episode 1 of the OVA.
- A new scene is of Isamu and Lucy at a dock, where he does his pre-flight movements from Episode 2. It also leads up to a new scene to after Lucy and Isamu had slept together.
- This new scene is also an alternate version of a scene when Sharon Apple makes a phone call to both Isamu and Guld warning them about a fire at the concert hall. In this version Isamu had just woken up and Lucy (clearly naked) is in bed with him. The original version simply had Isamu gazing at a computer monitor and repeatedly pressing the letter "M" when he gets the phone call. At the end of this version of events, Isamu's relationship with Lucy is implied to not have gone any further.
- After the joint test flights of the YF-19 and YF-21, (the montage from Episode 2) it is revealed that Isamu's reckless flying rendered the YF-19 unfit for testing and had to be taken for repairs. This explains why Isamu is flying a VF-11 during another test flight of the YF-21. (This is essentially the test flight from Episode 1)
- Isamu gets injured during a test flight of the YF-21, not in a melee with the YF-21. This is the same test flight that is featured in Episode 1 (in which Isamu is flying a VF-11 with rocket booster packs), right up to when Guld forces Isamu's VF-11 into the ground causing him to lose control and crash, with the major injuries he sustained forcing him to be sent to hospital. (In the OVA Version, Isamu escaped injury with barely a scratch) This scene replaces the original grudge match at the climax of Episode 2 when both pilots were using their test craft in melee combat, which ended when Guld, pinned to the ground by a rampaging Isamu, uses Isamu's Gunpod (Guld had intentionally replaced Isamu's blank ammo with live ammo in an earlier scene in the OVA) and shoots Isamu's craft at close range, which gave him the severe injuries he was being treated for in hospital.
- After Guld goes after Isamu (who had stolen the YF-19 to take on the new X-9 Ghost Fighter) a new scene features Col. Millard and Lucy staring at the night sky. Millard talks about his hopes for Isamu.
- At the Sharon Apple concert at Macross City, a new scene and song is inserted to replace what was the ending of Episode 3 ("After In The Dark," the ending theme for the first 3 episodes of the OVA), and the opening song of Episode 4 titled "Pulse." The new song is "Wanna Be An Angel," and includes new animation of Sharon Apple flying through the whole city. This then leads back into the song "Information High."
- The conclusion of the dogfight between Guld and the X-9 Ghost is extended, with Guld's body being crushed under the extreme G-Forces and a final image of his head exploding in his helmet before finally crashing into the Ghost fighter. Guld is then seen drifting into orbit.
- Sharon Apple sending Isamu into his dream-like state is extended with more footage of him flying towards the SDF-1. When Myung sings and wakes up Isamu, Sharon attempts to take Isamu back, only to have Isamu smash his head on the forward console to stop Sharon from appearing.
- After the SDF-1 lands back in the lake, Sharon has a final lament before dying. Afterward, Isamu and Myung are seen standing on top of the Macross watching the sunrise. Isamu then tells Myung that her singing helped him to win, ending the film with Myung singing "Voices".