In the distant future, Earth has been devastated by the Great Catastrophe, a global disaster that altered the planet's geography and climate. Humanity is now under constant threat from the Shadow Angels, an ancient race that has reawakened to reclaim Earth. To combat this threat, the organization DEAVA (Dimension Energy Active Vanguard Agency) deploys giant mechas called Aquaria, which are piloted by young individuals known as Element Users. These pilots possess unique abilities tied to the elements and must merge their powers to form the powerful mecha Aquarion, a weapon capable of defending humanity.

The story centers on Apollo, a feral and carefree young man with mysterious origins, who is discovered to be a potential Element User. Apollo is brought to DEAVA, where he meets other pilots, including the disciplined and stoic Sirius and the compassionate Silvia. The trio forms the core of the Aquarion team, with Apollo's unpredictable nature often clashing with Sirius's rigid demeanor. As the pilots train and battle the Shadow Angels, they uncover deeper connections between Apollo and the ancient conflict, hinting at his possible reincarnation as Apollonius, a legendary hero who fought the Shadow Angels 12,000 years ago.

The narrative explores themes of reincarnation, destiny, and the power of human emotions. The Shadow Angels, led by the enigmatic Toma, seek to harvest human emotions to sustain their existence, viewing humanity as both a resource and a threat. As the battles intensify, the pilots of Aquarion grapple with their own fears, desires, and relationships, particularly the growing bond between Apollo and Silvia, which echoes a tragic love story from the past. The series balances action-packed mecha battles with introspective moments, delving into the characters' personal struggles and the broader implications of their fight.

Throughout the series, the concept of "vectoring" is central, symbolizing the merging of minds, bodies, and spirits to achieve greater power. This theme is reflected in the pilots' need to overcome their differences and work together to unlock Aquarion's full potential. The story culminates in a climactic confrontation between Apollo and Toma, revealing the true nature of their connection and the ultimate fate of humanity. The series concludes with a resolution that ties together the threads of past and present, leaving a lasting impact on the characters and their world.