Final Fantasy: The Spirits Within - Storyline

The film opens in the year 2065, where a future Earth is infested by Phantoms, alien life forms who upon physical contact with human beings extract, consume and thus seemingly destroy their souls. The remaining humans live in "barrier cities" all over the world and are engaged in an ongoing struggle to free the planet. Two scientists, Aki Ross and her mentor, Dr. Sid, are searching for eight life forms which they believe possess spirits capable, when joined, of defeating the Phantoms. Meanwhile, a general named Hein is determined to use a powerful space cannon to destroy the Phantoms, though Aki and Sid believe the cannon may destroy the Earth.
Aki was infected by a Phantom during one of her experiments, but with the help of the first five spirits, she was able to contain the infection temporarily. Searching for the Sixth Spirit in the ruins of New York City, Aki is cornered by Phantoms, but is rescued by a team led by Gray Edwards who was once romantically involved with Aki.
When they return, Aki and Sid appear before a leadership council along with Gen. Hein where they debate the use of the space cannon. Aki wins more time but only by revealing that she has been infected, convincing Hein that she is being controlled by the Phantoms. He has three men placed with her as she and Gray's squad travel to find the Seventh Spirit. They succeed in finding it, but are attacked by Phantoms in the process and they realize that the Phantoms are attracted to Aki. Hein's men attempt to arrest Aki but in the ensuing struggle and attacks by phantoms, they are killed and their souls are destroyed. Meanwhile Aki's infection worsens and she falls unconscious.
Gray's squad takes Aki to Sid's lab where Sid helps Gray to join Aki's dream. In the dream, they witness a war on an alien planet. The war ends when terrible explosions rip the planet apart and Aki realizes that the Phantoms are the spirits of the dead aliens brought to Earth on a fragment of their planet. They awake as Sid uses the Seventh Spirit to bring the infection back under control.
Meanwhile, Hein uses the incident with the Seventh Spirit to gain access to Sid and Aki's personal possessions and sees the images of the aliens in Aki's dream recorder. With this evidence, he has Sid, Aki and Gray's squad arrested.
In an attempt to ensure that the council will give him clearance to fire the space cannon, Gen. Hein takes control of the barrier shielding the city from the Phantoms and lowers it until they start to enter. Though Hein intended that only a few of the Phantoms enter, his plan backfires, as the Phantoms use plasma conduits to invade the entire city.
With the city under an evacuation order, Sid, Aki and Gray's squad are released from detention. They attempt to flee the city but only Sid, Aki and Gray escape with their lives in Aki's spaceship. Sid scans for the Eighth Spirit and finds it at the crater where the fragment of the alien planet collided with the Earth. Meanwhile, Hein escapes as well and, guilt-ridden and suicidal, boards the space cannon where he finally receives authorization to fire it, lying to the surviving council members as to the reason the Phantoms were able to invade the city.
Sid lowers Aki and Gray into the crater in a shielded vehicle so they can locate the Eighth Spirit and combine it with the others. They are about to succeed when Hein fires the space cannon into the crater, not only causing the Phantoms to mutate and grow larger, but causing the Eighth Spirit to disappear.
Aki has another vision of the Phantom home planet where she receives the Eighth Spirit. When she wakes, she and Gray combine it with the other seven and use the shield on their vehicle as a projector for them. When a Phantom touches the shield, it begins a chain reaction which neutralizes all of the Phantoms.
Meanwhile, Hein disables the cannon's safety mechanism and fires it again, destroying the cannon and everyone aboard it. The beam hits the Earth's spirit, or Gaia, the existence of which was long a pet theory of Dr. Sid. Gaia is damaged and angered, just as the spirit of the alien planet was damaged and angered when that planet was destroyed.
Aki still has the eight spirits though and, with the vehicle destroyed, Gray sacrifices his own life and soul to transmit them directly to Gaia. Gaia is returned to normal as the destructive energy is beamed back into space. The movie ends with Aki being pulled from the crater holding Gray's body and looking into the newly liberated world.