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Dog Days takes place in the world of Flonyard, an alternate world where its inhabitants look like humans but with animal ears. When Cinque Izumi suddenly gets summoned to this alternate world he is appointed as a Hero. How will he lead his life and interact with the various characters in this new world?

Takamachi Nanoha is a normal third-grader who feels a little useless and out-of-place with no purpose. Then one day, she saves a ferret, who turns out to be a mage from another planet who came to this planet to search for the jewel seeds. Nanoha agrees to help, but this task gets complicated when another girl arrives to steal them.

Yuuno Scraia is a mage from a distant planet working to fix the problem he started when Jewel Seeds were accidentally spread around the world. In a failed attempt to seal a seed properly, he winds up on Earth in the form of a ferret. However, his battle with the seeds did not end upon reaching the Earth and he needs somebody else's help to seal the seeds for him. Takamachi Nanoha hears his telepathic cries for help and comes to his rescue. When she is given a pearl known as the Raging Heart she is able to transform into Magical Girl Lyrical Nanoha and wield a staff to fend off the evil that lies within the Seeds. In order to help Yuuno complete his mission, she needs to seal all 21 Jewel Seeds away, but Fate may be playing a hand in the matter to prevent Nanoha's goals.

Six months after the events of Magical Girl Lyrical Nanoha: The Movie 1st, Fate has returned to Uminari City with Lindy as her legal guardian and is living the life of a normal elementary schoolgirl along with Nanoha and her friends. The reunion between the two new-found friends is cut short, however, when they are assaulted by four ancient magic users who identify themselves as the Wolkenritter. As the motives behind the actions of the Wolkenritter become clear, Nanoha and Fate find themselves in a race against time to stop the reactivation of a highly dangerous artifact known as the Book of Darkness.

As the conflict that began in Magical Girl Lyrical Nanoha: Reflection continues to escalate, Nanoha and her allies soon find out the troubled history between Iris and Yuri, which is related to the tragedy of Eltoria's "Planet Reclamation Committee".

The planet Eltria, having suffered severe desertification in the past, has all but been abandoned. Against her older sister's wishes, Kyrie Florian travels to Earth alongside her best friend, the AI Iris, in search of the key to their planet's regeneration. However, the only way to find it lies within the Tome of the Night Sky, leading them into conflict with Nanoha and her friends.

Thirty years ago, aliens attacked Earth and nearly brought humanity to extinction. Since then, mankind has clawed for survival, fighting the invaders for land, and the UN established EXCEEDS, an agency to stave off alien threats. On a remote island in a world of chaos, young hunter Shiina yearns for a quiet life with her sister, Setsuna, but a single incident draws her into the larger battle.

The story is set in the future, not long after the present day. Hyper Sports, which use extreme gear as support items, have become popular hobby competitions among both children and adults. Hiyori Hayama is a high school singer who has nothing to do with Hyper Sports, but a certain incident sets the story in motion.