"The movie starts with a dream. A young
woman stares at a barren landscape. Something rumbles in the
distance, quietly at first then building to a deafening
intensity. As the source of the sound rushes to overtake her, she
awakes. Her name is Aki (Ming-na), and she has been having this
same dream over and over as she orbits the Earth in her space
shuttle. Though she does not know what it means, she believes she
can find the answer on the surface of the planet...but she must
save it first.
New York, Times Square. Aki searches amongst the rubble and trash of what was once a great city. She carries a small scanner with her, and appears to be scanning for something called "the sixth spirit." As she focuses on her work, she is slowly surrounded by "grossly asymmetric creatures, translucent, with enormous brains and tentacle arms." These ghost-creatures are the Phantoms, and they are not friendly. Suddenly, a blinding light comes from above, and the troop transport of the DEEP EYES begins unloading its soldiers. They open fire on the Phantoms, vaporizing them in bursts of electrical discharge. The Leader of the team attempts to get Aki on the ship, but she looks at her scanner and runs away. Searching through the ruined buildings, the DEEP EYES chase after her. She insists that a life form exists in the city, and she will not leave until it is found. And find it she does: a tiny weed growing in a crack. As she transfers it to a container, Phantoms begin to rise from the floor and pass through the walls all around. The soldiers fire desperately, but there are just too many Phantoms. Another blinding light streams down; the transport has found them again. They quickly climb out of the ruins and onto the transport, just before the phantoms get them.
On the transport, the DEEP EYES remove their helmets. Neil (either Steve Buscemi or Ving Rhames) is a wise-cracker, never takes anything seriously. Jane (Peri Gilpin) is a gung-ho soldier who is a little defensive about her gender (think Vasquez in Aliens). The third soldier is Ryan (either Buscemi or Rhames), and is only slightly less sarcastic than Neil. The leader does not remove his helmet at first, but when Aki confronts him, he reveals himself to be Gray (Alec Baldwin). Aki obviously recognizes him, and is rather shocked to see him.
At Barrier City (where an energy barrier keeps the phantoms out), it is discovered during their entry security scan that Gray has come in contact with a Phantom. That is all it takes to cause an infestation: one touch and you're dead, as is everyone around you. Gray is locked inside a quarantine tube as they pass into the city, but his friends bust him out and Aki straps him to a nearby operating table (they keep emercengy rooms by the security checkpoint to try to save infested people as they come in). Gray has less than 3 minutes to live as Aki starts burning out the infestation with a laser. Gray barely makes it.
When the excitement calms down, the security tech trys to scan Aki for infestation, she looks aprehensive about this, but Dr. Sid (either James Woods or Donald Sutherland) arrives and clears her through without a scan. They go to a lab where they take the "spirit" from the plant and fuse it with five other spirits. They display the energy pattern of the 6 spirits, and it almost matches another display: the energy pattern of a Phantom spirit. This pleases them very much, and as Aki leaves, Sid tells her to stay away from Gray, lest the become romantically involved. You get the impression that were involved once before.
Aki dreams again, and this time the rumbling is revealed as two Phantom armies hurling themselves at each other.
Council Hall. Day. General Hein (either Woods or Sutherland) is trying to convince the council to use the Zeus, an enormous space energy-cannon, to blast the Phantoms at their source: a meteor that crashed into the Earth in 2031. Sid stands and demostrates how the Zeus will indeed wipe-out the Phantoms, but may also destroy the Gaia, the Earth's spirit. The council laughs at the idea of the Earth having a spirit. Sid ignores them and reveals his plan: by gathering spirits from Earth creatures, he is building an energy that is the exact opposite of the Phantom's energy. This energy can be used to "cancel out" the Phantoms. The council is skeptical, but Aki bursts out that she has proof, that a terminally ill patient has been able to contain the infection, though has not yet been cured. She then reveals that her chest is encased in a metallic device. Turning on a display, she reveals herself to be the terminally ill patient. Her body is one giant infestation, but she is still alive due to the energy produced by her mechanical chestplate. Gray, sitting in the back of the room, shows no emotion.
Later that night, Aki continues her research from a gondola above the barrier that covers New York. Gray shows up and decides to tag along, but Aki ignores him. On the ground, Ryan and Niel try to create a romantic mood by fiddling with some wires and stranding Aki and Gray over the city. Gray brings up the past, how Aki disappeared without even saying goodbye, and Aki tell him about how she was infected, and about the spirits she's gathered. Gray gets all romantic, and they have a touching moment that is interrupted by the sudden re-starting of the gondola.
Hein summons Gray to his office, and assigns the DEEP EYES the task of watching Aki for aberrant behavior. He worries that the Phantoms are controlling her mind. Gray, ever the good soldier, agrees.
Aki dreams of the battle again, but this time the battle suddenly stops and all the aliens look towards her. She turns around and screams. Awake, she decides that the infestation must be gaining the upper hand.
Aki, the DEEP EYES, and several other soldiers fly over an old battlefield where human kind once fought the Phantoms. The land and quickly search for the 7th spirit, which they discover is actually an energy pack on a dead soldier. They grab it and try to leave, but the Phantoms have surrounded them. They run like hell for the ship, and Aki passes out. As they try to take off Neil realizes that the ship is being straddled by a giant spider-like Phantom. He does some fancy flying all over the battlefield (think: cool action sequence). Meanwhile, in the back of the ship, the nameless soldiers turn on Gray and demand custody of Aki. She's dreaming again, and this time she sees what terrified her last time: a wall of fire sweeping over the alien battlefield. She awakes with the scream, and a startled soldier shoots her. The DEEP EYES attack, but a soldier recovers his gun. Just then, Neil flies the ship through the leg of a giant Phantom. The ghostly leg passes through the cabin and right through the soldier, who immediately stiffens and dies.
Back in Barrier City, Sid and Gray work to fuse the 7th spirit directly into Aki to keep her alive. Gray enters Aki's dream and the two of them experience the final fate of the alien planet. As the operation is finished, Hein's men storm the room and arrest the DEEP EYES, Aki, and Sid. They have already destroyed Sid's lab. Hein then shuts down a part of the barrier so the Phantoms can invade some the city. He wants to pretend like the barrier failed so the council will let him use Zeus. In prison, Aki reveals what the meteor relly is, and what the Phantoms really are. You'll all have to see the movie for that little secret! Hein and his men watch as Phantoms invade one sector of the city. But wait! The Phantoms are now spreading outside of that sector. They're spreading everywhere! As they frantically search for an answer, they all suddenly stop and look up...at the huge overhead pipes running through all the buildings in the city. "