In the futuristic metropolis of Graviton City, built within the crater left by an ancient alien spacecraft crash, a red-haired high school girl named A-ko Magami possesses superhuman strength and speed, though she considers herself otherwise normal and mostly worries about being late for class. She lives a carefree life with her bubbly, childlike best friend C-ko Kotobuki, whose constant need for protection and tendency to attract trouble forms the center of A-ko’s daily routine. Their peaceful school existence is upended when the wealthy and brilliant B-ko Daitokuji transfers to their school. B-ko quickly develops an obsessive infatuation with the innocent C-ko, viewing A-ko as the only obstacle to winning the blonde girl’s affection.

What follows is an escalating war between A-ko and B-ko that unfolds each morning on the way to Graviton High School. Using her family’s vast resources and her own genius for mechanical engineering, B-ko constructs increasingly massive and outlandish mecha to crush her rival, only to see each one effortlessly destroyed by A-ko’s raw power. Their rivalry, which B-ko reveals dates back to a bitter competition in kindergarten, culminates in B-ko donning her skimpy but powerful Akagiyama-23 battlesuit for a direct confrontation that demolishes much of the school and a significant portion of the city. Midway through this chaotic battle, a gigantic alien spaceship from the Lepton Kingdom of Alpha Cygni arrives, having tracked their long-lost princess to Earth. The aliens, led by the trench-coated operative D and the alcoholic Captain Napolipolita, identify C-ko as their missing royal and attempt to abduct her.

The conflict escalates as A-ko and B-ko, forced into an uneasy truce, storm the alien vessel to rescue C-ko. A-ko fights through D and the Captain while B-ko retrieves their friend, though B-ko immediately betrays the alliance and attacks A-ko once C-ko is safe, accidentally destroying the ship’s navigation systems. The disabled spacecraft crashes, coming to rest precariously atop the very alien wreckage upon which Graviton City was built. In the aftermath, A-ko and C-ko return to their daily routine, walking to school past the now-stranded aliens begging for donations to repair their ship, while B-ko watches from a distance, already planning her next attack.

The manga narrative extends beyond this initial confrontation into several distinct story arcs. Project A-ko 2: Plot of the Daitokuji Financial Group shifts focus to B-ko’s father, the trillionaire industrialist Hikaru Daitokuji, who manipulates the military into attacking the grounded alien ship to seize its technology, forcing the girls to intervene. Project A-ko 3: Cinderella Rhapsody takes a more romantic turn as A-ko takes a part-time job to afford new clothes and meets Kei, a handsome biker, sparking a three-way competition for his attention between A-ko, B-ko, and the surprisingly central C-ko. Project A-ko 4: Final brings the series to a close as another alien fleet arrives to retrieve their princess, while Mr. Daitokuji arranges a marriage between Kei and their teacher Miss Ayumi, leading A-ko and B-ko to fight over a boy for the final time while C-ko, feeling neglected, considers leaving Earth with her people. An additional two-part alternate universe story, A-ko the VS: Grey Side and Blue Side, reimagines the characters as space-faring bounty hunters in a separate continuity, suggesting the rivalry between A-ko and B-ko is a constant across all realities. Throughout these arcs, the manga functions as a dense parody of 1970s and 1980s anime and manga conventions, with background gags referencing everything from Fist of the North Star to Superman and Wonder Woman, the latter implied to be A-ko’s secret parents. The title itself is a reference to the Jackie Chan film Project A.