BLAME! (Buramu!), by Tsutomu Nihei. First published in 1998 and first published in 2005.
PLOT:
Killy is a lone man wandering endless levels of destruction, the remnants of some unknown superstructure. There are rumors of survivors in the levels above, but from where Killy stands all he can see are mutants, killer robots, and a few scattered groups of humans struggling to survive. All of these parties may be part of a larger conflict with a body known as The Authority, but Killy isn't interested in that. All he knows is that he needs to find the Net Terminal genes - those from a time before the mutations started - and that he must continue to climb upward if he is to survive.
