The story of Cross, a youth whose body was augmented with cyborg units against his will in an effort to create the ultimate military soldier. But, as an early prototype of Cyborg-Human augmentations, Cross' Installations Could not be controlled properly and Cross was deemed as a failed experiment. He remembers nothing before the procedure, but remembers a female counterpart who underwent the same procedure.
The cyber additions to Cross' body slowly spread and consume him, as well as his humanity. Afraid of himself or his friend slowly being consumed by these horrible cyber installations, Cross searches for both the girl and the engineer responsible for the atrocity.
Cross' eye is an orange-red, or Vermilion. His Vermilion eye allows him to download power-ups and abilities from computer terminals to be used in conjuction with with his beam gun.
Upon finally finding the girl, he finds that she is almost entirely consumed by her cyborg-part, and is forced to kill her. To preserve what humanity he has left, he rushes to find a way to rid himself of the augmentations.
He comes into contact with a girl who's known and cared for him for some time. She gradually begins to introduce him to their memories that they had together as friends, and Cross begins to remember his past before the procedure, and through his feelings for her, he overpowers the cyber installations of his body, but ultimately must face off against the engineers as well as other "failed experiments"....and finally, his own cyborg persona.
In the end, Cross finds love, overcomes his machine persona, and regains his memories and humanity. The game will end with a zoom in to Cross' now blue left eye, symbolic of his freedom, and everything that makes him human.