Nine is set in the year "202X", taking place during the latter half of Shin Megami Tensei and in the time leading up to its sequel Shin Megami Tensei II. In the wake of the ICBM attack on Tokyo, communities of survivors now live in underground cities. In the face of their predicament, the underground inhabitants create "Idea Space", a virtual world based on Tokyo from the 1990s. The protagonist, named Kei Azuma by default, is exploring the virtual world when "Noise", digitized demons hostile to humans, appear and begin attacking Idea Space players through their avatars. After fending off an attack, Azuma is employed by the Central Administration Bureau as a Debugger, a player who traverses Idea Space and repels Noise invasions. During their missions through Idea Space, Azuma meets with multiple characters: Baraki/Sumire, a childhood friend who represents "Chaos", Mubiora/Miranda, a representative from the Central Administration Bureau who represents "Law". While going through their duty as a Debugger, the events of the latter half of Shin Megami Tensei take place, which culminate in all parts of Tokyo being destroyed in a Great Flood triggered by the God-worshipping Order of Messiah: Azuma survives due to their body being in cold storage, meaning that their mind becomes linked to Idea Space along with their Law and Chaos allies.
During a mission into the virtual Shibuya 109 against the Noise demon Abaddon, the true origins of Idea Space are revealed. Idea Space was created by humans tired of awaiting the arrival of their "Messiah" in the real world: hoping to bring about salvation through technology, the humans created the Idea Space, and generated Maria as its goddess and administrator to further the creation of Millennial Kingdom by manipulating its users. On their mission into Shibuya 109, Azuma retrieves a Desire Disc, an artifact containing the saved desires of humanity that is the key to both sides' plans. Azuma is faced with choices about which faction to support. The Law faction, supported by Maria, wishes to bring peace to humanity along with releasing the Idea Space's inhabitants. The Chaos faction, which can be led by Lucifer if he is freed from his prison within a metaphysical plain called the Expanse, intends to destroy the inhabitants of Idea Space and start anew with the chosen Adam and Eve: Azuma and the Chaos companion. To fulfill any of their chosen roles, Azuma must defeat Yaldabaoth, the controller of Idea Space who is keeping the system going and will not allow either Maria or Lucifer to carry out their plans.
In both the Law and Chaos routes, with the defeat of the Yaldabaoth, the entire Idea Space is emptied of avatars besides Azuma. Upon returning to the real world, they are on the surface with either their Law or Chaos companion, with the Messian-built Tokyo Millennium in the background: depending on the alignment, Azuma either goes to reinforce the Law-based regime, or to begin a new Chaos-based humanity outside it. In the "Neutral" routes, Azuma performs tasks for a mysterious woman minding a store in Idea Space: the woman is the goddess Sophia, who was forced to reincarnate as a human for the sin of birthing Yaldabaoth: she has been helping Azuma towards defeating Yaldabaoth to atone for her sin and ascend. Azuma defeats both Yaldabaoth and Maria, allowing Sophia to become her true self and ascend, leaving the fate of those within Idea Space ambiguous.
