The film takes place on a certain isolated island, at a certain middle school, and on the eve of the culture festival. A boy quits baseball after playing his whole life and has a fight with his best friend. Then, they suddenly meet a mysterious, red-eyed girl named Noruda, and a huge typhoon hits the middle school.

Second film of film trilogy. At the last stronghold of humanity, the Heavenly Crest (Astronomy) Club, Akio learns the fate of the world. Two pilots are needed to battle the two remaining Usurpers which are targeting the faded Fire of Life. During the battle against the second enemy, during the curse of happy times, the choice between the happy present and the future Akio must dedicate her soul to approaches.

Yorn gazes up at two massive cities floating in the sky and dreams of discovering their mysteries. Without warning, those mysteries come looking for him. Edenic assassins murder his father and Yorn is next on the hit list. A nameless old man and a mysterious young girl help Yorn on his quest to find his long-lost mother and the truth. Known as the God Hunter, Yorn leads a race against the dark designs of the technological overlords.

Though Hibiki and crew defeated a super-huge battleship of the earth in the last of the first stage, they noticed five battleships further aiming at Mejeiru and Tarahk. And, crew of NIRVANA learnt Tarahk and Mejeiru which were their home had been faced to the crisis of Karitori (reaping). Travel to their home is speed up so that they may inform of the crisis. On the way, current information of the earth having been brought by girl Misty who had come to travel with them was worse than they can imagine. Hibiki and crew noticed a true fight was in the future. VANDREAD is finally changed into final system by the attack of the enemy who becomes violent more and more. Can they save their home? And, what happens to the relations between Hibiki and Dita?