Dr. Ross is a scientist in the post-apocalyptic mid-21st century who has been infected by a race of aliens called Phantoms, that landed on Earth and are destroying all life on Earth. Even though she is dying because of her experience with the aliens, she now has the ability to link herself to their secret of survival, through strange recurring dreams, and how she can use it to help the remnants of humanity fight the xenomorphic parasites who seem to be sucking the souls out of the surviving population.
She has now allied herself with the "Deep Eyes Squad", a specialist troop of soldiers who are determined to eradicate the alien menace once and for all. Aki is charged with finding the eight special spirits which are supposed to help save the planet. (from The Final Fantasy Wiki)