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.

When the Shadow Angels invade after 12,000 years of slumber, humanity is held captive by fear and sheer alien dominance. Eleven years after the Great Catastrophe decimated the world, most of those left alive are scavengers, dirty and starving in the streets. There is hope, however: Mechanical Angel Aquarion! 
 
Powered by three souls intertwined, a rare breed of pilot takes the controls. Known as Elements, one among them must rise if mankind is to survive. Prophecy is being fulfilled as the end of the world approaches... Through a swirling cloud of love, betrayal, loss and destiny, the last hope for the new century arrives and takes flight! 
 
(Source: Funimation)

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