It is the year 2065, and Earth has changed drastically from what it once was. Lethal alien beings called Phantoms have emerged across the globe, and simply touching them is fatal, resulting in either immediate death or a slow deterioration. To attempt to save the remnants of humanity, massive force-field barriers have been erected around specific cities to keep the Phantoms at bay. Scientists Aki Ross and her mentor, Dr. Sid, are searching for a lasting solution to this invasion. Their research has uncovered a type of spiritual, Gaia energy capable of eliminating the Phantoms from the world. Aki and Sid are not alone in their mission within Final Fantasy: The Spirits Within; the human council and the military unit "Deep Eyes" are prepared to assist. However, not everyone supports this approach. Aki, Sid, Grey, and their companions must unite against both alien and human threats if they hope to restore peace to Earth. While the Phantoms, whose touch is deadly, seem like the greater danger, they will discover that their human adversaries are equally formidable.