In deep space a battle wages between the forces of good and evil and the fate of the Earth hangs in the balance. The evil Neos Gold dispatches her invading forces towards Earth with only one aim: the total destruction of all mankind. Now it's up to Iczer 3 (the younger sister of Iczer 1) to defend the Earth from the deadly armada of Neos Gold, with only the Earth's single remaining battle cruiser on her side. But don't count her out; what Iczer 3 lacks in experience she makes up for in all-out enthusiasm.

After the break up of their old band, guitarist Yuki & drummer Santa decide to form a new one. They recruit bass player Towa, young guitarist Atsuro, and after much persuasion, vocalist Sakuya. Together they form Lucifer and they struggle to make it in the music business, and also to stay together. As well, they have to deal with personal issues, such as parental objections, and watching their old bands succeed ahead of them. Sakuya is the most troubled band member, as he has to deal with his tragic past, and his relationship with teenaged lyricist Aine.

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.

Bonus segments of Cinderella Girls Gekijou 2nd Season streamed on The iDOLM@STER Cinderella Girls Mobage following the television broadcast.