In the year 2065, Earth is overrun by phantom-like alien entities known as the Phantoms, which have devastated the planet, leading to humanity's near extinction. The surviving humans have taken refuge in "barrier cities," protected ecosystems shielding them from the harmful environment outside and Phantom attacks. Dr. Aki Ross, a brilliant young scientist, and her mentor, Dr. Sid, are on a quest to find a way to defeat the Phantoms. They believe that gathering spirit wave patterns from biological organisms will help them create an "energy wave" that can neutralize the Phantoms without harming the Earth.

To aid them in collecting the wave patterns, they team up with the Deep Eyes military squad, led by the disciplined Captain Gray Edwards. As Aki continues her mission, she is also fighting a personal battle – she's infected by a Phantom and is struggling to keep the infection at bay using an experimental energy shield that Dr. Sid created. While the military, led by General Hein, favors a more aggressive approach to combat the alien threat by using the powerful Zeus Cannon, Aki and her team argue that such action could result in the destruction of the planet. The tension rises between the factions as Earth’s fate hangs in the balance, with each side desperate to save humanity in their own way.