In the late 19th century, as the cruel times of the Bakumatsu period came to a close, a new Meiji era marked the age of restoration for Japan. With the war over, its infamous hero Hitokiri Battousai disappeared into thin air, leaving only his legend behind. Years later, a seemingly plain wanderer named Kenshin Himura encounters Kaoru Kamiya, the owner of a struggling local dojo in Tokyo. Kaoru pursues a self-proclaimed Battousai who roams the streets, indiscriminately killing citizens and police officers. Furthermore, the warrior professes to use the Kamiya Kasshin-ryu—a sword style developed by Kaoru's father deeply rooted in the essence of life, not death. Kenshin decides to help Kaoru take down the impostor and restore her father's dojo. Unbeknownst to all, Kenshin is none other than the real warrior whose name still terrifies the people. Although Kaoru eventually learns the truth, his oath to atone for his murderous history by bloodlessly protecting the weak moves her, and she welcomes Kenshin to stay at her dojo. However, Kenshin's ideals are soon challenged by ghosts of the past and enemies of the present.

At the end of the calendar 2020, the continent of Stern, which has reached the end of civilization due to the exhaustion of magic elements, ushered in the destruction of the continent under the void storm. Ye Xuan, the last god of law in the mainland, unexpectedly awakened in the era of the prosperous magic civilization three thousand years ago and became an ordinary student at the Sith Magic Academy on the border of the Kingdom of Orlando in the northwest of the mainland. In order to save the mainland and prevent the end from coming, Ye Xuan began to explore the mystery of the dark turmoil that led to the depletion of magical elements in the mainland three thousand years ago, to prevent the mainland crisis.

In order to prevent the catastrophe called the Grand Fall, Rid Hershel and his companions Farah, Keel and Meredy have obtained the three Greater Spirits ("Craymels" in the game version) of Inferia. En route to Mount Farlos, Rid is kidnapped by the bounty hunter Marone Blucarno, and the party is compelled to head to Belcarnu, an archipelago far from the major cities of Inferia. A series of adventures forces them to remain on the islands, where a more immediate threat to Inferia sleeps.

Hatanaka Kosaku, a hopeful boxer, has a mean KO punch. Unfortunately, his dietary willpower is weak, and he eats even greasy hamburgers right before a bout. As a result, he has to compete in higher weight classes, and as soon as he takes an abdominal punch, he vomits, which causes him to lose the match in shame. As he tries to grapple with his weak will, he meets Sister Angela, a novitiate at a local convent. While Sister Angela strives to help Hatanaka in his endeavor, he seems to make her training to be a nun more difficult.