The story of the Japanese version of Electrosphere takes place on Strangereal's Usean continent in 2040.[7] By this time, Usea's national governments, while still present, have been effectively replaced by multinational corporations. The most powerful of these corporations are the rivals Neucom Incorporated and General Resource Limited; both have their own military forces and claims to territory on the continent.

Sometime in the 2030s, territorial disputes between Neucom and General Resource began to escalate. The peacekeeping Universal Peace Enforcement Organization (UPEO), under the authority of the Neo United Nations, has maintained relative peace between the corporations. At the start of the game, Neucom performs large-scale strikes against General Resource, pushing UPEO to use force to prevent further escalation, leading to a three-way war. As the game progresses, a terrorist organization named Ouroboros is revealed to have sparked the conflict between the two companies.

The player takes control of Nemo, ostensibly a new recruit for UPEO. As the story progresses, the player is given opportunities to defect from UPEO and join Neucom, General Resource, or Ouroboros. These decisions change the path of the story, the fates of multiple characters, and the ending the player receives. After the player witnesses all five endings, a final cutscene reveals that Nemo was actually an artificial intelligence created by Simon Orestes Cohen. The entire Intercorporate War was a simulation Simon designed to test whether an artificial copy of another character, Abyssal Dision, would be killed in the war. Since all five endings result in the AI Dision's death, Simon is pleased with the results and is assumed to release Nemo into the real world.