In a post-apocalyptic world, humanity faces constant threats from shadowy beings known as the Abductors, who harvest human life energy. To combat this, the organization DEAVA employs young pilots to operate powerful mecha called Aquaria, which can combine into the legendary machine Aquarion. The story centers on Apollo, a feral and carefree boy with mysterious origins, who is discovered to possess the rare ability to pilot Aquarion. His arrival disrupts the established dynamics within DEAVA, particularly affecting the disciplined and reserved Silvia de Alisia, who shares a deep connection with Apollo through recurring visions of a past life.

As Apollo integrates into DEAVA, his interactions with Silvia and her twin brother, Sirius, reveal a complex web of reincarnation and destiny. The narrative explores themes of love, sacrifice, and the cyclical nature of existence, as the characters grapple with their intertwined fates. The Abductors, led by the enigmatic Toma, seek to harness the power of Aquarion for their own purposes, leading to escalating conflicts that test the resolve of Apollo and his comrades. Throughout the series, the past lives of the characters are gradually unveiled, revealing their roles in a tragic love triangle that spanned millennia.

The plot intertwines mecha battles with emotional and philosophical undertones, as the pilots of Aquarion confront not only external enemies but also their inner struggles and relationships. The series culminates in a climactic confrontation that forces the characters to make profound choices about their identities and the future of humanity. The narrative balances action, romance, and introspection, creating a multifaceted story that delves into the enduring power of love and the consequences of destiny.