Three hundred years ago, a genetic experiment gone wrong caused the mutation of all forests on Earth. Armed with consciousness, the vegetation sought to destroy all of humankind, and the war that ensued turned the planet into a hellish dystopia. In the present day, Agito, a young boy, lives with his father in Neutral City—a village maintaining an uneasy truce with the neighboring forest. One day, Agito, on his way to collect water, becomes separated from his friend and stumbles upon a relic of the past: a girl sleeping in a mysterious machine. Agito awakens the girl, Toola Cm Sacl, and introduces her to the village. But outside forces have ulterior motives for the girl, who holds the key to restore the Earth. Misguided by Shunack, a soldier from the old world hellbent on destroying the forest, Toola follows him despite Agito's warning. Determined to save Toola and unify humankind with the forest, Agito borrows the power of the forest and pursues her.

In the far future, the elevated irradiation from the sun has destroyed the environment of the earth and the birthrate of humans has drastically decreased. The government controls society with an army of cloned soldiers called Ideal Children (IC). Sam Coyne is a trader in a desert. One day, he saves a beautiful woman Maya, who has been chased by Theseus, a corps of IC. He shelters her in his trade ship, but the destroyers of Theseus surround Sam and Maya.

Although traumatized by witnessing the murder of his parents by one of the Choushuu, Ichimura Tetsunosuke's thirst for revenge lead him to desire strength. At the age of 15, Tetsunosuke approached the Shinsengumi, wanting to become one of its members. However, Tetsunosuke lacked the skill, mind and will to emotionlessly cut down whoever threatened peace and the Shinsengumi. Even with the support of his brother Tatsunosuke and his newfound friends of the Shinsengumi, little did Tetsunosuke know the blood and pain he would have to face being part of this historical group.

Three years ago, the long war between the Royal Empire and the Republic of Frost came to an end. With both nations a long way from recovery, a passionate young woman named Alice L. Malvin leads the Pumpkin Scissors, a unit of the imperial army specializing in war relief. During a mission to assist a village occupied by renegade soldiers, Alice meets Randal Oland, a scarred former soldier with a sordid past and kind heart. Encouraged by the efforts of the Pumpkin Scissors, he joins the team on their mission. During the assault, however, Randal enters a trance-like state prompted by a mysterious blue lantern. As a result, he acquires monstrous strength and decimates the enemy forces. Despite having witnessed Randal's disturbing transformation, Alice invites him to join her squandrant, confident that his gentle nature will prevail and make him a perfect fit for the Pumpkin Scissors.