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.

Toshokan Sensou tells the story of Kasahara Iku, the first woman to join the Library Task Force. In the near future in Japan, the Media Enhancement Law has been forced upon the population censoring all books and media. To counter this, the Library Defense Force was created. To protect themselves against the Media Enhancement Law Commission, all major libraries are fully equipped with a military Task Force, who take it upon themselves to protect the books and freedom of media of the people. This anime follows Iku and her fellow soldiers as they protect various special books and artifacts from the oppression of the Media Enhancement Law Commission. A love story, war story, and comedy all rolled into one.

Kasahara Iku and Dojo Atsushi receive an emergency recall in the middle of their date as Japan is rocked by a terror attack. Their new duty is a protection detail assigned to Touma Kurato, an author. Meanwhile, the relationship between Librarians and the Media Purity Committee is also worsening.

An unaired episode included in the Toshokan Sensou DVD volume 3, and later on Blue-ray Box (June 8, 2012) that celebrates the airing of Toshokan Sensou Movie. Komaki was arrested for the violation of human rights of his girl friend Marie, who had difficulty in hearing. He was kept in custody and tortured by the Media Improvement Forces. The members of the Task Forces made a desperate effort to rescue him.