After a decade spent fighting monsters in the Shadow Labyrinth—a growing dark cloud of magic that threatens to engulf the world and destroy all life—mage Desir Herrman and his five companions finally face their last foe: the dragon of destruction Boromir Napolitan. Although the group of heroes manages to slay this formidable opponent, the tremendous amount of mana stored within the dragon's body is released in an unstoppable explosion that annihilates the rest of the world. However, instead of dying, Desir is sent back 10 years into the past with complete memories of events to come. He enrolls at Hebrion Academy, determined to put an end to the classist prejudice plaguing the magical world that will ultimately lead to the demise of humanity. Unfortunately, his struggle begins early on during the entrance exams; although he is ranked first of his group, Desir is assigned to the Beta Class, the default class for commoners. Now, Desir's next objective is to rally someone to his cause that he could not save in his previous life: the wind mage Romantica Eru. Then, Desir will have to show his worth to the Alpha Class with his newly formed party if he wants to ultimately save as many lives as possible.

In the final match against the Kanagawa street racing team Sidewinder, Project D street racer Takumi Fujiwara is faced with a surprising challenger: Shinji Inui, a 17-year-old high school student. Beginning to drive at a very young age, Shinji is not only familiar with the mountain pass where the race is taking place, but he also drives a Toyota AE86—the same car model Takumi uses. Initially reluctant to participate due to a lack of enthusiasm, Shinji becomes motivated after witnessing the fiery battle between Keisuke Takahashi and Gou Houjou. Undefeated in his home course known as the Tsubaki Line, Shinji might prove to be Takumi's most formidable opponent yet.

As they continue their journey through the Johto region, Satoshi and his friends visit Altomare, an island city that hosts an annual racing event called the Pokémon Water Race. While Takeshi and Kasumi are enjoying themselves, strange things seem to be happening to Satoshi—he somehow loses the water race, sees some women attack a girl with their Pokémon, and despite them saving her, the girl later denies ever seeing Satoshi and Pikachu before! Fortunately for Satoshi, his confusion clears up as he learns that the girl he and Pikachu saved earlier was actually a Pokémon named Latias, who likes to disguise herself as her human friend, Kanon. Latias and another Pokémon, Latios, are known as the Eon Pokémon, as they inhabit and guard Altomare along with a mystical blue sphere called the Soul Dew. An ancient legend of Altomare is highly connected to the Eon Pokémon and the Soul Dew, and is well known among the locals—as well as among Latias' earlier assailants, the thief sisters Zanner and Lyon. As the thieves attempt to capture both the Eon Pokémon and the Soul Dew, Satoshi is forced to act in order to stop them from bringing disaster to Altomare.

The technology to create powerful cyborg soldiers has been released for public use by the Berühren Corporation. Those outfitted with robotic parts are known as the Extended. Juuzou Inui, one such Extended, was created as a soldier and has no memories of his former life. But now, after the war, he runs a business that takes care of Extended-related incidents around the city. Rumors of a renegade Extended that kidnapped a child reach his ears; lo and behold, as Juuzo returns to his office, a giant robotic man with a boy on his back crashes in, asking for help. While Juuzou could just turn the guy in and be done with it, something about this situation is too fishy to ignore. It seems that everyone wants hold of this kid and, whether he likes it or not, Juuzou must find out why this Extended is on the run, how it connects to the Berühren Corporation, and just how far the treachery runs in this city.