Twelve thousand years after the events of Genesis of Aquarion, mankind living on the planet Vega (ヴェーガ Vēga?) is threatened by a new enemy from the planet Altair (アルテア界 Arutea Kai?) whose female population was wiped out by a mysterious disease. The Altians using their "Abductors", just like the Shadow Angels, invade the cities in Vega to kidnap its inhabitants looking for females strong enough to survive the inter-dimensional travel back to Altair to ensure the preservation of their race.