Over three hundred years have passed since the Calamity War, the great conflict between Earth and its outer space colonies. Now Earth is ruled over by four economic blocs, and the military organization Gjallarhorn is responsible for keeping the peace. Mars, on the other hand, depends heavily on Earth's economy. Horrified by the appalling living conditions that Mars' inhabitants have to bear, Kudelia Aina Bernstein, a young aristocrat from the Chryse Autonomous Region, gets involved in the Red Planet's independence movement. She hires the services of a local company, Chryse Guard Security (CGS), to escort her on the journey to Earth to negotiate economic conditions with the earthly bloc that controls the region. The Third Army Division—consisting of Mikazuki Augus, Orga Itsuka, and many other child soldiers—are chosen to protect her. When Gjallarhorn attacks the CGS facilities to assassinate the young revolutionary threatening their interests, Orga and his comrades must not let the attackers accomplish their goal—in fact, Gjallarhorn's actions might turn out to be the unintentional catalyst that leads the children to be the forgers of their own destiny.

For the Takakura family, destiny is an ever-spinning wheel, pointing passionately in their direction with equal tides of joy and sorrow before ticking on to the next wishmaker. With their parents gone, twin brothers Kanba and Shouma live alone with their beloved little sister Himari, whose poor health cannot decline any further. On the day Himari is given permission to temporarily leave the hospital, her brothers take her out to the aquarium to celebrate, where the family's supposed fate is brought forth with her sudden collapse. However, when Himari is inexplicably revived by a penguin hat from the aquarium's souvenir shop, the hand of fate continues to tick faithfully forward. With her miraculous recovery, though, comes a cost: there is a new entity within her body, whose condition for keeping her fate at bay sends the boys on a wild goose chase for the mysterious Penguin Drum. In their search, the boys will have to follow the threads of fate leading from their own shocking past and into the lives of other wishmakers vying for the Penguin Drum, all hoping to land upon their chosen destiny.

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.

With five new kids and an exciting new mission in the Digital World, Digimon Frontier brings back all the great action and adventure of the last three seasons. Takuya, Kouji, Izumi, Junpei. and Tomoki meet each other in a train that takes them to the Digital World where a war against evil is being fought. The Angel digimon, Cherubimon, one of The three angels sent to save the World from the power-hungry Lucemon, has turned to the dark side and the entire Digital World is in peril. To fight this great battle, the five CHOSEN ONES must find the Densetsu no Spirit (Legendary Spirit).