The Alpha Cygnans—still searching for their "lost princess"--return to Earth, this time with a fleet of three thousand ships. A-ko and B-ko continue their rivalry, especially over Kei, which leaves C-ko feeling left out. A-ko and B-ko have even more reason to scrap when Hikaru Daitokuji arranges a marriage between Miss Ayumi and Kei.
The wedding takes place at the gymnasium at Graviton City High School for Girls. At the same time, the Alpha Cygnan fleet—with their Queen on the flagship—approach the City, trying to stop the wedding. The weakened Earth Defense Force try to stop them from stopping the wedding. While all this is happening, A-ko and B-ko tear apart the wedding and try to do so to each other. Kei, Ayumi, and C-ko are caught in the middle of the melee.
Interspersed with the main narrative are cuts of an archeological team in Iraq, deciphering some apocalyptic writings at an ancient site that may or may not have something to do with the approach of the Alpha Cygnans.
- Miss Ayumi is seen grading her class's homework. One piece of paper is seen to have the puzzling words (No team orders whatsoever! Tension extreme daring attack at McClaren? Fuck you! Kill Jap! No more Hiroshima!! Senna takes second straight win on city street GP's? Oh! my son met her gay girl...) No explanation for this odd string of phrasing is currently available.
- The two children aged versions of A-ko and C-ko that run past C-ko at the movie theatre transform into children versions of Lum and Ran-chan from Urusei Yatsura.
- The official translated name for the movie C-ko watches is "Orange Angel: I want to return to that world" which is a parody of Kimagure Orange Road: I Want To Return To That Day**. **One of the most famous scenes from that movie ( the breakup on the park bench ) is parodied on A-KO Final, with Ranma and Akane look-alikes (from Ranma 1/2) taking the place of KOR's Kyosuke and Hikaru.
- After the movie C-ko falls out of her bed, a single-frame "animator's gag" is shown in the Japanese version. It shows A-ko and B-ko nude and holding each other. This frame was removed in the original release of the US version but was returned for the DVD release.
- A reference to Maison Ikkoku by Rumiko Takahashi can be found near the ending where a distinctly Kyoko-like woman can be seen with her daughter, wishing upon the "star" falling from the sky.