On the continent of Vainqueur, a land of man and beasts, the holy nation of the East, Alistel is in a state of war with Granorg, a massive country to the West that is ruled harshly by Queen Protea. Alistel's land is slowly turning to desert while a strange disease, known as the "Sand Plague", is turning its people into sand. The ruler of Alistel, the Prophet Noah, insists this worldwide disease is the result of Protea's evil government. The people of Alistel thus believe they are fighting a holy war against Granorg.
One day, Stocke and his subordinates, agents with the intelligence agency of Alistel, are sent into Granorg territory to rescue a secret agent who was captured by the government of Granorg. After saving the agent, the group find themselves surrounded by the Granorg army, and Stocke is severely wounded. He awakens in Historia, a world where time and space are warped. There, two mysterious children, Teo and Lippti, give him the ability to travel through time and space using the power of a book his employer Heiss gave him, the White Chronicle. After using this new power to travel through time to avoid defeat, Stocke is given a choice: continue working under Heiss in the intelligence division, or join his friend Rosch's unit within the military. Each choice creates a timeline and each timeline has its own separate story, which nonetheless relates to the other one. Stocke is often forced to move between timelines to acquire skills and information he would not otherwise have access to, in order to avoid disasters, ambushes or simply to position himself properly to take advantage of his enemies or friends.
Under Heiss, Stocke is sent to Granorg to assassinate Princess Eruca. He only manages to enter the city by pretending to be part of a group of traveling entertainers, most of whom are Satyros, one of the native beastmen races of the continent. Among them are Aht, a nine-year-old shaman who, for better or worse, begins idolizing Stocke and using her abilities to protect him. Once he arrives in Granorg, he discovers that the princess knew he would be coming, and moreover, had not informed anyone else. Stocke learns that Eruca is the de facto leader of the resistance against her stepmother's reign, and is therefore more an asset to Alistel's war on Granorg than an enemy. Eruca also reveals that she is the only living descendant of the empire's rulers, and thus the only person who can perform the ritual to prevent desertification. However, as Queen Protea refuses to allow her to perform the ritual, the world could turn to sand in less than a decade unless Protea is removed from power.
Stocke refrains from carrying out the assassination, thus securing her support. Oddly enough, he is also aided in this regard by his appearance, which is similar to Eruca's late older brother, Ernst, who was executed by her father for treason. Despite his best intentions, his failure to complete his mission brands him a traitor in Alistel, and General Hugo orders his execution.
In the other timeline, Stocke is assigned to Rosch's unit and deployed to protect Alistel's mines from enemy sabotage, as well as protect a cavern which is the only route connecting the two mountainous territories of Granorg and Alistel, other than a slim valley protected by the oft-traded Sand Fortress. After successfully defending the mines, Stocke and Rosch are rewarded by General Hugo with promotions, but he also assigns them to the Sand Fortress with a platoon of new recruits. Alistel's second-in-command, Lt. General Raul, assumes this is to remove any possible future political opponents from the city, as Field Marshal Viola, who also was gaining popularity against Hugo's will, was also assigned there. After defeating the Granorg army in two battles, Rosch's entire brigade is killed. Stocke then discovers a piece of paper proving that the Granorgites were being leaked information from within Alistel.
Stocke returns with the critically wounded Rosch to Alistel, and, taking the advice of Lt. General Raul, sneaks into Hugo's office to search for evidence of deals with Granorg. He finds a coded note that he believes to show the truth, and promptly flees Alistel with Raul, Rosch, and Rosch's doctor, Sonja. They arrive in Celestia and learn that Hugo had a secret pact with Protea's advisors, Dias and Selvan, to eliminate Protea from the throne, annex Granorg, and then conquer the entire continent. Stocke convinces Rosch to become the commander of Celestia's army, and Celestia prepares for war against Granorg and Alistel.
In the history created by Stocke refusing to leave Heiss, Stocke finds asylum in the desert nation of Cygnus, and convinces King Garland the Mighty to prepare for war against Granorg. Eruca then takes him to meet the Gutral tribe, who only meet with humans if they bear the sacred "Beast Mark". Stocke acquires the Mark, and recruits the Gutrals to fight against Granorg. They depose Protea, in doing so obtaining the "Etherion", a Granorg treasure that can neutralize a weapon designed under the orders of Hugo that turns its victims to sand.
Stocke returns to the other timeline, recruits the Gutrals using his Beast Mark, and enters the annexed Granorg with the Etherion. After defeating the Dias Knights and reluctantly killing Viola, who chose to remain loyal to Alistel because she believed that the death of her, the Valkyrie, would convince its troops to give up their fight, Stocke discovers that Hugo has been forced into confession by Alistel citizens that Noah was dead the whole time. Stocke pursues Hugo to Alistel and slays him.
In the final chapter of the "True History", created by both timelines combining, Heiss invades Granorg's Royal Hall, where the ritual to stop desertification is performed. Stocke confronts him, and Heiss explains that the sacrificial victims of the ritual are royals who were killed by their own family, and brought back to life by giving them part of their sibling's soul. During the ritual, the Sacrifice dies again, and the half of a soul returns to its original body, stabilizing the Mana of the continent, and thus slowing desertification, in the process. Stocke is, Heiss explains, Eruca's late brother Ernst, who was executed by his father King Victor for treason, given a part of a soul by Eruca for use in the ritual, and then captured by Heiss, who was Victor's brother and an intended Sacrifice himself, and had his memories modified so he'd live the life of Stocke.
Heiss believes that the suffering of the royal family, which he has seen as a Sacrifice, and thus a wielder of the Black Chronicle, is caused by their attempts to protect a world that is not worth saving. He plans to recruit Stocke to his side, leaving Eruca as the only living member of the royal family without any Sacrifices to use, but Stocke refuses. Heiss then attempts to absorb enough souls to hasten desertification enough to destroy the world altogether, so Sacrifices will no longer be necessary. He fails, and uses the Black Chronicle to take the party to Historia, which, along with the Chronicles, was created with the intention of enlightening Sacrifices, resulting in the ritual being more effective. He then consumes the suffering of all past Sacrifices, and becomes the monster Apocrypha, which is destroyed by Stocke and his allies.
If the player has not done sufficient sidequests, the game ends with Stocke being sacrificed by Eruca to prevent the desertification. However, it is possible to unlock a better ending, in which the player can see the major characters continuing to live out their lives; most notably, Raynie promises to wait for Stocke to return, Viola survives her wounds and is cured of an illness she became afflicted with on the front lines, and Rosch and Sonja are married, and encounter the soldiers in Rosch's brigade, whom they thought all dead. One of the soldiers explains a man who is implied to be Stocke rescued them. Heiss and Stocke wait in Historia during this ideal ending, and Heiss forcibly sacrifices himself instead of Stocke, seeing the difference Stocke made to the lives of the characters affected by the aforementioned sidequests, and realizing the world is worth saving. Stocke then returns to the real world.