"Sidonia no Kishi" (Knights of Sidonia) is a science fiction anime series set in a distant future where humanity has been driven to near extinction by a mysterious alien species known as the Gauna. The remnants of humanity reside aboard the massive seed ship Sidonia, a self-sustaining vessel that has been traveling through space for centuries. The story centers on Nagate Tanikaze, a young man who has lived his entire life in the ship's underground levels, isolated from the rest of society. When he is discovered and brought to the surface, his exceptional piloting skills quickly draw attention, leading to his recruitment as a Guardian, a pilot of the advanced mecha units called Gardes, which are used to combat the Gauna.

The Gauna are enigmatic, nearly indestructible beings that attack Sidonia and other human colonies. They are capable of mimicking human forms and technology, making them a persistent and evolving threat. Nagate, despite his inexperience with surface society, becomes a key figure in Sidonia's defense, working alongside other pilots such as Shizuka Hoshijiro, a skilled and compassionate teammate, and Izana Shinatose, a genderless individual who develops a close bond with Nagate. The series explores the dynamics of Sidonia's society, which has adapted to its precarious existence through genetic engineering, cloning, and a rigid hierarchical structure.

As the story progresses, Nagate and his fellow Guardians face increasingly dangerous encounters with the Gauna, including a massive Gauna known as the "Placental Hoshijiro," which takes on the form of a deceased comrade. These battles reveal more about the Gauna's nature and their connection to humanity. Sidonia's leadership, including the enigmatic Captain Kobayashi, who has ruled the ship for centuries through cloning, plays a crucial role in shaping the strategies and policies that determine humanity's survival. The series also delves into the moral and ethical dilemmas faced by Sidonia's inhabitants, such as the use of genetically engineered soldiers and the sacrifices required to sustain their way of life.

The narrative balances intense mecha combat with themes of survival, identity, and the resilience of humanity in the face of overwhelming odds. Nagate's journey from an isolated outsider to a pivotal figure in Sidonia's defense highlights the challenges of adapting to a society on the brink of extinction. The series concludes with a climactic battle that tests the limits of Sidonia's technology and the resolve of its people, leaving questions about the future of humanity and its relationship with the Gauna unresolved.