BLAME! 3 by Tsutomu Nihei

Cibo has uploaded herself into Sanakan's body, and she struggles to suppress Sanakan's consciousness and the Safeguard commands. Cibo and Kyrii continue their hunt for the Net Terminal Gene inside of Toha Heavy Industries, which appears to be a safe space where neither the Administration nor the Safeguards can interfere. Mensab is one of the few AIs who succeeded in protecting her human charges from the deadly attacks of the Silicon Life. Mensab attempts a forwarding that shunts Kyrii into an unstable space within Toha, where time and space warp at random, and he encounters a familiar face...