In the year 2065, the Earth is under attack by alien intruders, that came here by a meteor. Once colliding on the Earth, the aliens, called Phantoms by humans, destroys cities. And those who lived in the cities, gets their spirit pulled from their body, rendering in instant death by the Phantoms. The few humans that survived the onslaught by the aliens, hide behind barrier cities, invented by Dr.Sid and only venture out to keep the phantoms at bay. Now, Dr. Aki Ross, who's infected by a Phantom and Dr.Sid has found a way to rid the Earth of Phantoms using spirits that can cancel the Phantom force. However, General Hein, wants to stop the Phantom infestatations at all cost, even if it means the Earth itself. Now, Dr. Ross along with the Deep Eyes, military team, has to find all the spirits and vanquish the aliens before the time runs out. She discovers the truth about the Phantoms in her reacurring dream, while trying to find the spirits and trying not to get killed by Phantoms, in this action filled, and memerizing Final Fantasy.