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In the year 2079 AD, the mysterious mechanical cell clusters, know as Worms, begin the Human Being Sweep Operation. After a two-year war, one-third of the human race was wiped out. Finally setting national differences aside, in desperation, mankind reluctantly decides to use weapons of mass destruction. However, the victory against the Worms came at an enormous price: All the major continents were broken apart, Antarctica disappears, and half of the remaining land masses were submerged. Additionally 90% of the military personnel died, namely men in their twenties and thirties.Three years later, the supposedly destroyed enemy shows signs of activity again, near Midway. Special Vessel Koryu is sent in to reconnoitre, carrying three Sonic Diver unit fighters — the Aviation Exoskeleton Sky Divers:Reijin, Fujin, and Raijin, piloted by the Sky Girls, Sakurano Otoha, Sonomiya Karen, and Ichijou Eika respectively.The battles with an unfathomable enemy will challenge the three young, courageous test pilots to their utmost...

In the near future, Earth is at war with aliens called Worms. The war leaves the population of Earth decimated, with young men the main casualties. The Worms were beaten back but their re-emergence heralds the creation of a mecha unit called the Sonic Divers, piloted by 3 young girls to counter this threat.