This movie is an alternative version of the TV series; it is composed of the two 2007 OVAs, edited to improve the pacing of the plot, and an extra segment akin to a TV episode where the cast are given the task of studying flowers. The plot has several differences to the TV series, most important being Sirius's death at the beginning, Apollo's different childhood and the more marked focus on the events of 12000 years ago, particularly Apollonius' death and Reika's previous incarnation's involvement.

Set in the future, a giant fighting machine called the Aquarion is humanity's only effective weapon in the fight against the technologically advanced species called the Shadow Angels.