Plot
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Before the game begins, it is explained that everything in the real world was discovered to be composed of data on a quantum level. The Embryon tribe have emerged from the Junkyard with physical bodies due to the intervention of God. In the real world, the sun has turned black, resembling an eclipse, and sent out malignant "solar data", causing those exposed to be petrified. People with the Demon Virus, however, are immune. Cielo is taken hostage by the Lokapala, a resistance group against the powerful Karma Society, which sends out soldiers possessing the Demon Virus to harvest humans to devour. The Embryon manage to convince the Lokapala's leader, Roland, to free Cielo and join the team, and are also accompanied by Fred, the son of the former leader.
The Embryon infiltrate the Karma Society's city, which is protected by a giant sun-shield. After releasing all the prisoners from the Detention Facility, they try to rescue Sera from the Medical Ward, but discover a trap set up by Madame Cuvier, the Society's leader, who has brainwashed Heat into fighting the party. While Cuvier plans to impose a new world order, she is secretly opposed by Jenna Angel, the Chief Technical Director and antagonist of the previous game, who wants to use the Demon Virus to weed out the weak.
The Embryon reach the E.G.G., a giant device used to communicate with God, and rescue Sera; however, Heat shows up and critically wounds Serph, sending them both into the device itself. As God begins to absorb the entire planet, Angel murders the despondent Cuvier. The remaining team shut down the Power Plant, but are unable to stop the E.G.G.. Angel releases Meganada, which Roland and Argilla sacrifice themselves to kill, and Sera gains Serph's Atma. The team re-enters the distorted E.G.G. facility and defeat Heat's new form. Serph, who was kept alive by the device, has details about the past revealed to him by a black cat named Schrödinger.
A group of scientists founded the Karma Society to study God. Children who had the psychic ability to speak with God were located, and the scientists created the E.G.G. to enhance their power. However, many of the children were driven insane from prolonged exposure to God and die. Only one survived: candidate number 19, a girl named Sera. One of the scientists, Heat O'Brien, rebelled against the project because of Serph's unethical treatment of the test subjects. A fight ensued, and Sera accidentally witnessed Serph's true, evil nature, which he had hidden from her. After God felt Sera's sadness, he caused the sun to turn black and flooded the world with data, turning people into stone. Serph, becoming a demon, devoured his colleagues. Due to Sera's direct link with God, the data of many of those who perished was "copied" into the Junkyard, creating new AI programs.
A virtual paradise was created by Sera to escape from the pain she felt having to live in the real world. Every person and every location are copies of what she had seen in her life or things she wanted to see. Her perceived personalities of Serph and Heat are polar opposites of their actual personalities, due to Serph's manipulation. However, the military found out about her virtual world and demanded that she turn it into a battle simulation program for developing combat AIs; thus her paradise became the Junkyard. Jenna Angel later used the Junkyard as a testing ground for her Demon Virus. Sera entered the Junkyard to try to stop her, as the human personalities of the AIs within began to awaken.
The Embryon rush to the airport in a final gambit for survival. Gale perishes while killing Angel, while Cielo dies protecting Serph and Sera's fighter jet. The two arrive at the HAARP facility, beaming their individual data to the sun, and, in the process, merging to form a supreme being called Seraph. Reunited as solar data, the team makes a final plea to God for salvation. Defeating Brahman, they are able to calm God and return the sun to normal. Seraph, reaching enlightenment, travels with Schrödinger to a different universe, while the others are reincarnated as children on the renewed Earth, with their caretaker and narrator revealed to be Fred.
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