Sixteen years after its destruction by a meteor, Graviton City has been rebuilt into a futuristic metropolis. However, this is of little concern to superpowered high school student Eiko Magami, who only cares about her best friend Shiiko Kotobuki and arriving at school on time. Unfortunately, the incredibly intelligent Biko Daitokuji intends to befriend Shiiko, taking Eiko's place as the Shiiko's best friend using any means she can. Biko decides that, to accomplish this, she must defeat Eiko in combat. In order to overcome her super strength and speed, Biko creates a mecha and challenges Eiko in front of their school gate. As the two commence their battle, an extremely large spaceship hovers over Earth, searching for something left behind.

Three weeks after the incident that left Captain Napolipolita's ship balancing on top of Graviton City, A-Ko and the gang go on summer vacation. While A-Ko ponders losing some weight and B-Ko devises another plan to defeat her redheaded rival to win C-Ko, Napolipolita and Spy-D experience severe homesickness - begging for a way to return to their home planet. Meanwhile, Hikari Daitokuji - B-Ko's father and the CEO of the Daitokuji Financial Group - arms the local military with new mecha to attack Napolipolita's ship and obtain its advanced technology.

Yuuta was 12-year-old boy, who had lost his father in the traffic accident one year ago. In the summer vacation, he visited a deserted dam deep in the mountains, where he had a good time with his father before. Suddenly a thunder storm occurred and he slipped on the ground. He lost consciousness and woke up to find a girl and an unfamiliar village. He time-traveled 30 years and reached a village, which sank at the bottom of the dam. This is Yuuta's precious memory of "another" summer vacation.

In Iraq, a group of archaeologists discover ancient relics that prophecize the coming of a superior race and the end of all civilization. Meanwhile, back in Graviton City, as A-Ko and B-Ko's rivalry over Kei intensifies, Mr. Daitokuji sets up an arranged marriage between Miss Ayumi and Kei. Furious over the engagement, both A-Ko and B-Ko do whatever it takes to prevent the wedding from going through. Little do they know that another alien fleet is on its way towards Earth.