Sometime in the future, strange alien beings called Phantoms have taken over the Earth, decimating the cities and killing most of the inhabitants by extracting their spirits. It's the observation of that latter fact that has led Doctor Sid (voice of DONALD SUTHERLAND), and his protégé, Doctor Aki Ross (voice of MING-NA) to come up with a unique but controversial way of trying to stop the aliens and thus reclaim Earth.
Believing all life forms to contain signature spirits that can be identified and contained, Sid and Ross have set out to collect eight organic specimens whose collective spirit forces should counteract those of the alien beings. Having collected six of those eight spirits, the two are racing against various aspects of time. For one, Aki is infected with the alien force and she's living on borrowed time, although her condition has given her the ability to dream about the aliens and their origins.
More crucial, however, is the fact that General Hein (voice of JAMES WOODS) - who believes their spirit theory to be nothing but nonsense - desperately wants to use the Zeus Cannon, a powerful, outer space laser, to defeat the aliens once and for all. However, he doesn't have full support of the remaining human council to unleash the dangerous force on the Earth below.
As Sid and Ross try to prove Hein wrong and save the Earth in a more peaceful fashion, they must not only contend with him and the small military force - led by Captain Gray Edwards (voice of ALEC BALDWIN) and consisting of Ryan (voice of VING RHAMES), Neil (voice of STEVE BUSCEMI) and Jane (voice of PERI GILPIN) - sent to accompany and watch them, but also the beings themselves that seem determined to suck the souls out of every human they encounter.