Eve burst error is set in modern-day Japan. The player controls two characters: a young, seemingly careless private investigator Kojiroh, and the special agent Marina. Kojiroh has been struggling to make a living as a lone PI, but now luck seems to smile to him: the director of the Eldian International School, Mr. Ko, asks him to find a missing painting, supposedly of great value. At the same time, Marina is hired by the ambassador of the fictional Middle East republic Eldia to protect his daughter Mayako from terrorists. Switching between Kojiroh and Marina, the player gradually finds out the connection between the two cases and plunges deeper into a mystery that involves political struggle, scientific discoveries, and horrifying murders.