Five separate worlds—Black, White, Green, Red, and Blue—are linked by the Halo and exist in a harmonious balance. However, the Halo suddenly opens in an event known as the World Connect, threatening to destroy the universe. Coming under attack by Ouroboros, an alien species that wishes to accelerate the universe's end, the five worlds recruit girls with special abilities called Exceed to defend against them. Saya Sougetsu, a young girl from the Blue World of Earth, is one such individual able to wield Exceed power. Believing this to be her chance to make a difference, Saya eagerly joins the defense force. There, she meets Amane Ayashiro, another girl from Earth, as well as a selection of fighters from the other worlds. Faced with a formidable foe, the girls must prove that their newfound bonds are strong enough to save the future.

After Earth was decimated by World War III, the ruins of civilization were rebuilt, with the futuristic city of Olympus standing out like a crown jewel. Overseen by the supercomputer Gaia and populated with an extremely large number of Bioroids—genetically engineered people designed to handle all administrative functions—Olympus affords its citizens lives free from all worries. However, a surge of crimes has been occurring within this seemingly utopian environment. In order to protect the people, Deunan Knute and her partner Briareos Hecantochires work for Olympus' Enhanced SWAT team, taking on the most violent criminal cases. When a group of terrorists threaten to destroy the Olympians' way of life, Deunan and Briareos swear to take them down—no matter the cost.

Based on the RPG game of the same name. Aurica Nestmile is a young Reyvateil, or singing maiden who feels her song magic is not of much use to anyone. From high up on the tower Ar Tonelico comes Lyner Barsett, whose airship is totaled upon impact with the ground. These two meet up, and in the search for someone who can repair the ship, end up helping both each other and themselves.