Chasing a runaway alchemist with strange powers, brothers Edward and Alphonse Elric stumble into the squalid valley of the Milos. The Milosians are an oppressed group that seek to reclaim their holy land from Creta: a militaristic country that forcefully annexed their nation. In the eye of the political storm is a girl named Julia Crichton, who emphatically wishes for the Milos to regain their strength and return to being a nation of peace. Befriending the girl, Edward and Alphonse find themselves in the midst of a rising resistance that involves the use of the very object they have been seeking all along—the Philosopher's Stone. However, their past experiences with the stone cause them reservation, and the brothers are unwilling to help. But as they discover the secrets behind Creta's intentions and questionable history, the brothers are drawn into the battle between the rebellious Milos, who desire their liberty, and the Cretan military, who seek absolute power.

After Tamahome is reborn into the real world as Taka Sukunami, it does not take long until he meets Miaka Yuuki again, leading to their romance blooming once more. However, the appearance of Ren Shigyou—a new student at Miaka's high school—disturbs their blissful days. Resentful of the happy lovers, Shigyou uses his unusual manipulative skills to quickly become popular and rally his classmates against Miaka and Taka. As Shigyou's followers unexpectedly attack the pair, the two end up falling from the school's roof into a red light and are transported to The Universe of the Four Gods realm. Returning to the place where Taka once lived as Tamahome, the couple learns that an evil demon is behind the recent events. To make matters worse, Taka risks disappearing from existence unless he recovers his previous life's memories, which are stored in seven jewels. Joining forces with their former companions, Miaka and Taka embark on a quest against the clock to retrieve the precious stones before it is too late.

During a visit to the National Library, Miaka Yuuki and Yui Hongo stumble upon a strange old book that casts a red light, sucking them inside its unfamiliar world. Upon arrival, the two encounter hostile slave traders and barely escape with the help of Tamahome—a powerful young man bearing a Chinese symbol on his forehead. But, a moment later, the red light returns and takes Yui away. Desperate to reunite with her companion, Miaka asks Tamahome for assistance. However, the situation escalates when the pair encounters the land's emperor, Hotohori, who believes Miaka is the foretold priestess of the kingdom's protector god Suzaku. By gathering the god's seven Celestial Warriors, the priestess can summon Suzaku and have all her wishes granted. Hotohori hopes this will save his country, and since it appears to be a fitting solution to the girl's problems as well, he convinces her to accept the role. Meanwhile, at the library, Yui realizes she has been brought back alone. Unable to intervene, she helplessly witnesses Miaka traversing through courageous trials as the mysterious book's heroine.

Three years after the defeat of Gargoyle and Neo-Atlantis, a new threat has surfaced bent on bringing the world under his control. Geiger, using advanced robot technology, is attempting to begin a world war, and take control of the devistated world after the destruction has stopped. Once again, Nadia and Jean must fight to save the world, only this time from itself. (Source: ANN)