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.

Ghostly, primordial beings known as Mushi continue to cause mysterious changes in the lives of humans. The travelling Mushishi, Ginko, persists in trying to set right the strange and unsettling situations he encounters. Time loops, living shadows, and telepathy are among the overt effects of interference from Mushi, but more subtle symptoms that take years to be noticed also rouse Ginko's concern as he passes from village to village. Through circumstance, Ginko has become an arbiter, determining which Mushi are blessings and which are curses. But the lines that he seeks to draw are subjective. Some of his patients would rather exercise their new powers until they are utterly consumed by them; others desperately strive to rid themselves of afflictions which are in fact protecting their lives from devastation. Those who cross paths with Mushi must learn to accept seemingly impossible consequences for their actions, and heal wounds they did not know they had. Otherwise, they risk meeting with fates beyond their comprehension.

An apocalyptic event has ravaged Japan, leaving nothing but endless sandy plains behind, and a strange rusting disease terrorizes the remnants of civilization. According to the government, the horrific state of the new world is the result of mushroom spores being spread by the likes of Bisco Akaboshi, labeled the Man-Eating Mushroom. But Bisco would beg to differ. In reality, he is a Mushroom Protector, determined to uncover the legendary Sabikui mushroom—said to be the ultimate cure for the rusting disease. Joining him on his quest are his giant crab Akutagawa and the kind doctor Milo Nekoyanagi, who is actively searching for a rust poisoning treatment for his sick sister. Despite the prejudice aimed toward him by the common folk, Bisco refuses to give up on his quest to purify the rotting world.

Serebii, a Legendary Pokémon known for its ability to traverse time, is hunted by an unnamed Pokémon poacher seeking to capture it. Yukinari, a young Pokémon trainer who enjoys drawing portraits of Pokémon, tries to protect Serebii after it stumbles upon him; but in the middle of its escape, both vanish without a trace. Forty years later, ambitious Pokémon trainer Satoshi hopes to sight rare Pokémon around his local area. White, a boat driver, takes Satoshi to his village. Satoshi is accompanied by his three closest friends: Takeshi, a former gym leader training to be a great Pokémon breeder; Kasumi, a young girl wanting to become a skilled Water-type trainer; and Pikachu, Satoshi's Pokémon partner and first comrade. Meanwhile, Yukinari and Serebii reappear in Satoshi's present time and run into his group. Masked Lord Vicious, the strongest executive staff member of Team Rocket, desires to capture Serebii. Using the Dark Ball, a variant of Monster Ball that corrupts the Pokémon caught within and draws out their maximum power, Vicious can transform innocent Pokémon into powerful and frightening obstacles—including Serebii itself! Placed in a tough position, Satoshi, Yukinari, and their friends must work together to defeat Vicious and save Serebii and themselves.