Iji and her brother Dan were visiting the military complex where their father works when suddenly, out of nowhere, an alien spaceship of the Tasen race bombards the facility with a weapon called Alpha Strike, killing almost everyone inside. When Iji finally wakes up, many months later, she feels different. A few of the remaining scientists have altered her body with nanotechnology the aliens brought along, as a final means to get a weapon to strike back. Entirely abandoned, her brother is the only one left to guide her from a far control room through an intercom. She can choose to remain in the room and die, or talk to the Tasen leaders and convince them to take their spaceship and leave.
Iji is a side-scrolling platformer with major role-playing elements and a heavy focus on the narrative. Iji needs to explore ten sectors to find the Tasen leaders, but the choice becomes complicated when another alien race, the Komato, becomes involved. Through cut-scene sequences, in-game logbooks and conversations with her brother, Iji can steer the outcome of the story, choosing to enter a truce with one of the alien races when she finds out more about their motives. Based on the actions, the dialogue and the logbooks, revealing the history and thoughts of several alien characters, are also changed during the game. The player is never presented with dialogue choices to influence the story, but it changes according to the actions during the levels.
The basic movement for Iji includes moving around, jumping, climbing ledges and ducking. She starts with a shotgun with unlimited ammo and a powerful kick, but soon other weapons are added to her arsenal, such as a machinegun, a rocket launcher, an MPFG devastator, a resonance detonator and more advanced nanotechnology. Most of the weapons require ammo, scattered around, and at specific stations they can also be combined into new guns, combining features from two sets into new ones.
Iji has basic health and armor, a jump and armor skill (upgradable) and seven main skills: health, attack, assimilate, strength, crack, tasen and komato. These can be upgraded at stations through a levelling system using orbs left behind by enemies or found in containers, but the progress is capped per sector. Choosing which skills to improve alters the course of the game as they cannot all be maxed out, making her a hacking expert able to get through wired doors and disabling enemies (a small mini-game) or brute strength as she kicks right through them. Even though the focus in on engaging enemies, she can choose to keep the killing to a minimum to pursue a specific course for the game. Scarce power-ups provide unlimited ammo, damage all enemies in the environment or make her partially invisible.
There are minor puzzle elements where she needs to get past specific barriers, operate consoles to open doors and find alternative routes. Almost all weapons used by the enemies of both alien races can also be wielded by Iji when she gets to combine the parts. There are sections where she can drive hovering vehicles called Tasen Shredders and there are a few boss battles. There are four difficulty levels and completing the game in several ways opens up extras such as a sound test, two mini-games, new game modes, a level selection, a new costume and more.