Many Years Ago:

• On an unknown alien planet, an extremely aggressive race fights a war so pitched it ends up destroying its own planet. A large chunk of it flies off into space, carrying with it several million of its inhabitants and fauna of various sizes. The flight through space kills all the living things on the chunk, but they are imbued with such malice and suffering that they become ghosts of a sort, made of energy patterns, with the ability to tear out the souls of any living being they touch. They can also "infect" a living person, growing from within him and taking over his body and soul.

Years 2031-2065:

• The planetary chunk crash-lands on Earth, unleashing these Phantoms on the planet. Chaos ensues, and millions die.
• Dr. Sid, New York City's primary leader in the emerging field of bio-etheric energy, determines the wave composition of the Phantoms. He helps to design a barrier which can keep these Phantoms out, as well as a way to actually damage the non-corporeal beings. Barrier cities begin to be erected throughout Earth.
• The military, led by General Hein (whose family was killed by the Phantoms) are vehement that the total destruction of the Phantoms must take place through force. They construct an enormous space-bound cannon called Zeus to target the meteor where the Phantoms make their lair.
• Dr. Sid's studies lead him to discover another approach. Since the Phantoms are wave forms, constructing a wave of the exact opposite pattern would cancel out the Phantom wave and neutralize it. He is also against using the Zeus cannon because of his realization that the Earth itself is alive, an entity he calls Gaia, and that Gaia is the source for life on the planet. The Zeus cannon would doubtless injure Gaia by forcing the Phantoms to burrow ever deeper within the earth, an outcome which would doubtless be catastrophic.
• Dr. Sid begins constructing a theoretical wave pattern. He divides the pattern into eight parts, which he calls Spirits. Only specific life forms may carry a Spirit, and this necessitates scanning the environs of New York to find one that matches the pattern he needs. On the very first mission, though, his protege, Dr. Aki Ross, is infected by a Phantom. Sid discovers that Aki herself holds the first Spirit, and is successful in containing the Phantom particles by surrounding it with that Spirit.
• Aki begins fighting for her life, and searches madly for the other Spirits. She finds another four, each time implanting the pattern into the chest plate containing her Phantom and thus strengthening the bond. Soon after, she begins to have extremely graphical dreams involving the destruction of the alien planet, but never quite understands what they are or where they come from. She records them for future study.

Year 2065:

• On her sixth mission, Aki is hampered by the intrusion of the Deep Eyes, a military patrol led by a man named Gray Edwards. (The other members are Neil Fleming, Ryan Whittaker, and Jane Proudfoot.) She manages to retain the sixth Spirit, held by a plant, but Gray is infected by a Phantom himself. Upon discovering the fact after returning to the barrier city, Aki is barely successful in destroying the Phantom particles before it gains control of Gray's body and soul.
• One last consul meeting is held, in which General Hein and Dr. Sid vy for their own ideas as to how the Phantoms may be defeated. Aki finally reveals that she has a Phantom inside her, contained by the six Spirits. Due to that evidence, the Zeus cannon is denied permission to fire until Dr. Sid has completed his research. General Hein has absolutely no belief that the Spirit wave may actually defeat the Phantoms, and conspires to destroy Aki's believability to the consul.
• General Hein assigns the Deep Eyes to watch Aki on her next mission. He tells Gray that he believes Aki may be under the control of the Phantoms, and if he observes any strange activity on her part, he is to arrest her. He notices Gray's hesitance, however, and assigns his own men to watch over the Deep Eyes as well.
• The seventh mission leads to a barren wasteland riddled with corpses from a previous battle. The Spirit they are looking for lies in a one-celled organism which powers the energy pack of a gun from a dead fighter. The Deep Eyes and Aki barely make it out alive, but Aki is having severe trouble controlling the Phantom inside her without the seventh Spirit. General Hein's men attempt to take control but are defeated by a combination of the Deep Eyes and a random Phantom attack. However, they damage Aki's chest plate with a stray bullet.
• General Hein searches Aki's room for any evidence he can use against her and comes across the records of her dreams. He issues a warrant for Aki, Sid, and the Deep Eyes; they are captured just after Dr. Sid succeeds in implanting the seventh Spirit into Aki and containing the Phantom within her.
• Hein takes a squad of his most trusted soldiers, including longtime compatriot Major Elliott, to the barrier control system. He believes that a small demonstration of the Phantoms' capacity for destruction is all he needs to win the consul over to his side at last. He deactivates one barrier panel, allowing Phantoms to enter the town. However, he underestimates the Phantoms' ability to travel through the energy streams powering the barrier city, and eventually the entire city is under attack and the survivors are evacuated. Elliott is killed by a Phantom before Hein's own eyes.
• The Deep Eyes, Aki, and Sid escape their prison, but only barely. Sid maintains that their only hope is to find the eighth Spirit and project it, cancelling all the Phantoms out. They steal a wheeled transport to travel there, but Ryan is wounded by a bumpy ride. He urges them to leave him there but to leave him a gun; they comply. The remaining Deep Eyes manage to reach Aki's ship, but while Neil leaves to detach a final coupling from the ship and Jane stays to protect him, they are both killed by a sudden Phantom attack. Ryan, who comes on the scene with guns blazing, is also killed. Gray's anger and sadness is such that he almost forces Aki to leave him there, but she saves him at the last moment.
• Dr. Sid discovers that the eighth Spirit belongs to a Phantom inside the Phantom Crater, the crash site. In a last-ditch attempt, Aki and Gray agree to go inside and capture the last Spirit.
• General Hein, overcome with remorse, resigns himself to suicide, but a thought strikes him just before he pulls the trigger. He instead decides to travel to the Zeus cannon and destroy the Phantoms for once and for all. On the way he receives a message from the consul members allowing him to do so.
• Hein fires the Zeus cannon before Aki and Gray can actually reach the eighth Spirit, and it is destroyed. As he continues firing, Aki and Gray see an enormous creature, whom Dr. Sid deduces is the Gaia of the alien world. They attempt to speak to Hein, dissuading him from continuing, but he refuses to listen. He continues to fire, the last shot entering the very heart of Earth's Gaia. However, as he continues to try to wreak havoc, the Zeus cannon overloads and the entire space station self-destructs.
• Aki discovers another eighth Spirit: the Phantom inside her, reacting to the closeness of Earth's Gaia. She hooks Dr. Sid's device to the shield around her transport; Phantoms which touch it are disintegrated. However, she still needs a way to project the wave. Gray, mortally wounded in the Zeus cannon attack, lets the alien Gaia steal his own soul, imbued with the eight Spirits, and spread it to the rest of the Phantoms, neutralizing them all. He then expires, while Earth's Gaia slowly revives itself.