Iji is described by Remar as System Shock 2 in 2D. Players control Iji Kataiser, an ordinary human female who has been enhanced with nanotechnology following the invasion of Earth by an alien species known as the Tasen., who themselves turn out to be running from their relatives, the Komato. Iji must navigate a research station while being guided by her brother Dan, who communicates via the station's loudspeaker system, in order to convince the aliens' leader to retreat from the planet.] Though the game's plot is linear, interactions with non-player characters change according to the player's actions, leading to one of multiple endings. The player's primary choice is between pursuing Iji's goal either as a pacifist or by engaging in violence against the Tasen and the Komato.
Iji's nanotech energy field functions as a shield, and players begin the game armed with a shotgun. Seven further weapons can be collected throughout the game; including a machine gun, rocket launcher and alien technology like the Shocksplinter weapon. Eight additional weapons can be unlocked by combining the standard firearms using a combining station, depending on her Crack ability. Blue nanofields that function as experience can be collected during play, when enough are collected Iji gains a level. Each level she gains allows the player to use an upgrade station to increase one of Iji's seven skills by one level. These skills include physical traits such as strength and health, as well as abilities such as close-quarters combat and computer hacking. Iji's jumping ability and armor can both be improved twice each during play if players can find their power-ups.