A thousand years after the destruction of Earth by gigantic aliens called Gauna, mankind is living on massive spaceships. One of these space ships is Sidonia, which is protected by large pilot controlled exosuits called Gardes.

After destroying Earth many years ago, the alien race Gauna has been pursuing the remnants of humanity-which, having narrowly escaped, fled across the galaxy in a number of giant seed ships. In the year 3394, Nagate Tanikaze surfaces from his lifelong seclusion deep beneath the seed ship Sidonia in search of food on the upper levels, only to find himself dragged into events unfolding without his knowledge. When the Gauna begin their assault on Sidonia, it's up to Tanikaze-with the help of his fellow soldiers and friends Shizuka Hoshijiro, Izana Shinatose, and Yuhata Midorikawa-to defend humanity's last hope for survival, and defeat their alien foes. Sidonia no Kishi follows Tanikaze as he discovers the world that has been above him his entire life, and becomes the hero Sidonia needs.—MAL Rewrite

The future is not favorable for humans anymore: our planet is no longer there, world population has decreased dramatically, because of the gauna invasion, and there is a chance that humans can be completely annihilated. However, humans are known for their ability to adapt and this time they will not give up that easily. Many seed ships are being created, which are later sent in different parts of space and are designed to be the last stronghold of the human race. Although, seed ships do have weaponry, they use robots called gardes, or guardians to protect the main ship from any possible threat that might occur. Not much is known about other seed ships, because the distance between them is so great that it takes more than 100 years only for one message to be delivered. In this lovely setting, Knight of Sidonia focuses on one of these seed ships. Sidonia has its own guardian Saitou Hiroki, who is a guardian's pilot and Sidonia's top 1 ace. However, one day, due to some unknown circumstances, Hiroki refuses to take medicine anymore, which increases the lifespan; he takes his grandson with him and hides from the people of Sidonia. Eventually, Hiroki dies and it forces his grandson to the surface. One of the Sidonia's leaders immediately understands that Nagate is the only grandson of one of the greatest ace pilots Sidonia has ever had and that his grandson is believed to be as skilled as his grandad and sends him on a mission. Right on his very first mission, Tanikaze faces the main foe of humanity that has not attacked Sidonia for a long while-gauna. Can Tanikaze defend Sidonia?—Scientiiaa