There is the exemplary manga Blame!, in which the intelligent machines have run amok and turned the whole Solar System into one dystopian megastructure, and the safeguard protocols, like an immune system gone awry, have wiped out the majority of humans. The hero is an agent tasked the reviving humanity, which requires him to embark on a centuries-long journey through this megastructure, which is something like Journey to the West meets the Odyssey.
https://en.wikipedia.org/wiki/Blame!