In the year 2065, the Earth is no longer a haven for the human race. A meteor has collided with the planet, carrying wraith-like alien life. These aliens have decimated the cities and forced the survivors hide in barrier cities. Dr. Aki Ross, a brilliant scientist, holds the key to reclaiming Earth, but General Hein, a man consumed by vengance for his murdered family does his best to stop Dr. Ross and the Aliens. He advocates the use of the powerful Zeus Cannon, but Aki, and her mentor, Dr. Sid, believe that the Cannon will kill off the aliens and permanently damage our planet.

The key to Aki's plan is the search for the final spirits required to make a spiritual rhythm - An energy wave in exact oposition to the energy pattern of the phantoms - that will neutralize the threat with no effect on any other living creature. As all life has been defined as types of energy, Aki's quest is to scan the entire planet to find the appropriate spirits .

If dealing with General Hein wasn't enough, Aki must still deal with the Phantoms themselves. The aliens come in every concievable shape and size, from humanoid to the Giant "Meta-class" behemoths. Despite their vast differences in appearance, they are all subject to the same hunger: life energy, be it human, plant, or animal. Any source of energy causes them to swarm, even the energy packs that power vehicles and weaponry. They aren't called phantoms for nothing, they easily pass through anything solid, ripping the soul from anything they touch. The only thing with the ability to stop them is an engery barrier, which lead to the construction of the barrier cities.

Will Aki, with the Aid of the Deep Eyes Military Squardon be able to assemble the Spiritual Rhythm? Or will General Hein gain the approval necessary to fire the Zeus Cannon?