Plot
Radiant Historia is set on the continent of Vainqueur, a land populated by humans and Beastribes. Once ruled by an ancient empire, it is now divided between the warring kingdoms of Alistel and Granorg; the root of the war stems from Alistel's belief that Granorg is responsible for the spread of the Sand Plague, a magical illness which drains living beings of their Mana energy and turns them to sand—the desertification of the continent is spreading, further inflaming the conflict. Stocke, an espionage agent for Alistel, is sent by his superior Heiss on a mission with mercenaries Raynie and Marco to escort a spy back to Alistel's capital; before leaving, Stocke is given a book called the "White Chronicle" by Heiss. The group are ambushed by Granorg troops, with only a severely wounded Stocke escaping. He is drawn into Historia, a realm divorced from time, and told by its overseers Teo and Lippti that he can use the White Chronicle to alter events. Stocke makes the mission a success, saving Raynie and Marco along the way.
Over the course of his adventure, Stocke follows two different timelines; one where he remains under Heiss, and one where he becomes part of a military unit led by his friend Rosch. He uses skills acquired in each timeline to proceed further in each role, while also interacting with the Beastmen tribes, particularly the young shaman Aht and the sympathetic warrior Gafka. During his travels, someone wielding the Black Chronicle—a twin to the White Chronicle—is trying to interfere with his efforts. In both timelines he aids and is aided by Granorg's princess Eruca, who is capable of performing a ritual to stop the Sand Plague consuming Vainqueur with a sacrificed human soul. He also learns that Hugo, a prominent religious leader of Alistel, has formed a pact with Granorg to depose its ruling queen Protea and is manipulating the war for his own ends; and that Heiss is acting for his own agenda, playing both sides against each other, and has intimate knowledge of the White Chronicle.
In both timelines, Stocke successfully overthrows Protea and defeats Hugo. Heiss then reveals that the ritual's sacrifices are Granorg royalty who are resurrected using part of another person's soul, then killed again to reunite the soul and stabilize Vainqueur's mana, slowing the Sand Plague. Stocke is revealed to be the intended sacrifice, Eruca's brother resurrected and given a part of Eruca's soul. Heiss, Stocke's uncle, believing the ritual and the sacrifice's suffering to be pointless, intends to let the Sand Plague consume Vainqueur; he abducted Stocke, gave him his present identity, and has been using the Black Chronicle to try and show Stocke the futility of the sacrifice's mission. From Heiss and Teo and Lippti, Stocke learns that the Sand Plague was caused by a runaway spell intended to stabilize the world's mana and ensure the prosperity of the ancient empire. The empire's surviving royalty created the Black and White Chronicle to facilitate the ritual, allowing the Sacrifice to see hope in the future while the Caster meditated on the past; Teo and Lippti are the remnants of the sorcerer who created the Chronicles. Heiss was the intended Sacrifice, but escaped with the Black Chronicle, which ingrained his fatalistic views.
After thwarting Heiss' attempts to change history in his favor, Heiss transports the party to Historia, fusing with the souls of past sacrifices to become the monster Apocrypha; Stocke and his party defeat Heiss while destroying Apocrypha. In the normal ending, Stocke willingly becomes the sacrifice, allowing the ritual's completion and delaying the Sand Plague's advance. In the true ending—unlocked by completing all events across the game—Heiss willingly becomes the sacrifice in Stocke's place upon seeing Stocke's unshaken faith in the future, allowing Stocke to return to the world and live a full life. The other characters work to help Vainqueur rebuild, including beginning research into ways of stabilizing mana which will negate the ritual and the need for sacrifices.
The expanded storyline of Perfect Chronology has Stocke interacting with a woman named Nemesia aboard a ship existing outside time; collecting artifacts, Stocke helps Nemesia bring together a third magical book dubbed the Red Chronicle with the aim of stopping the desertification. Once all the artifacts are retrieved, Stocke persuades Heiss to lend the power of the Black Chronicle, then reunites with the group and Nemesia. Nemesia reveals that the desertification is caused by a Mana-consuming entity dubbed the Singularity, created by the Empire's experiments on Nemesia's secret lover Rhodan when creating the Chronicles. Using the three Chronicles' combined powers, the party destroy the Singularity, negating the need for the sacrifice. Nemesia chooses to stay with the comatose Rhodan outside time. In their own world, the characters settle down to normal lives, with Stocke and Heiss parting as friends. Nemesia and Rhodan—who is beginning to recover from his coma—are brought into the real world by Stocke using a newly generated artifact from the Red Chronicle.