Infected by an alien, Dr. Aki Ross along with Dr.Sid has the means of destroying the Phantoms. Keeping her Phantom infestation at bay, by using the already found spirits to contain them. Aki, now must find the remain spirits to save the Earth as well as herself.
She's also having a reacurring dreams, that may be the truth of the Phantom force. Getting help from the Captain Gray Edwards, and his Deep Eyes squad, she searches the world for the spirits. While getting critizism from General Hein, who wants to destroy the Phantoms by using a more violent force, she is determined to find the spirits, so the Earth can have a future.