Iji Kataiser is the titular protagonist of the game, Iji. Once a normal human, Iji became a cyborg after she was wounded by a weapon called Alpha Strike, losing her father and her younger sister in the process. Now, enhanced with nanotechnology, Iji must deal with two different hostile alien species.
While at a science facility with her father and younger sister, a space weapon know as Alpha Strike was activated and hit the ground near the facility, killing nearly everyone, including Iji's father and sister. Some months later, Iji awakens and discovers that she was modified with alien technology by local scientists and researchers, she also discovers that her brother, Dan, is still alive and she has to speak with an alien called Krotera, a Elite Leader of a race of aliens named Tasen, whose she believes to be the responsables for the Alpha Strike. Shorty after, it was revealed that the Tasen invasion unfortunately is worldwide, and that another alien called Komato, rivals to the Tasen, are also invading the planet. She eventually finds Krotera but failed to convince him to stop the Tasen invasion, he tries to kill Iji but fails and is killed by Iji or depending on Iji's moral choices, by another Tasen named Vateilika. Before his death, reveals to Iji that earth was actually a Tasen colony, and that they are trying to escape from the Komato. Later, she meets a skilled Komato Assassin Leader named Asha, working under the behalf of a powerful and fearsome Komato General named Tor and his lover, a Komato Annihilator Leader named Iosa. Iji defeats him but Asha manages to escape. Shortly after, she finally finds Dan and he says that the Komato are trying to use the Alpha Strike again, in order to kill the remaining Tasen, with that in mind, Iji destroys another dangerous weapon named Phantom Hammer and a powerful Komato Sentinel named Proxima. However, a second Phantom Hammer was used by the aliens, completely destroying the shields protecting earth and allowing the Alpha Strike to do it's job. To make the situation worse, Asha finds Dan and kidnaps him, depending on Iji's moral choices, Dan is either saved by Iji or killed by Asha, no matter what happens, Asha manages to escape again. Iji eventually encounters one of Asha's superiors, Iosa, and fights with her, depending on Iji's moral choices, Iji is aided by a Komato Assassin named Ansaksie. After a long battle, Iosa is finally killed by either Iji or Ansaksie. Later, Iji has third encounter with Asha and kills him, though this fight can be prevented, and Asha commits suicide. Sometime later, Iji finally finds General Tor and argues with him, leading to a final showdown with Tor on the roof. Despite having extremely powerful weapons, Iji luckily manages to defeat him, leaving Tor alive, but severely wounded. Eventually, Tor agrees with Iji and cancels the Alpha Strike, saving earth and commiting suicide. With the Tasen and Komato gone, earth was finally in peace, completing Iji's mission.