This is the point where he realizes what he has done and what he has become. The nanites have rewired his brain, accellerating his intellect. But a side effect of this was that he could no longer deny the consequences of his actions before his transformation.

The guilt and regret caused him to engage in extensive self mutilation in an attempt to end his own life. The remorse he felt over the things he had done was too intense, and the physical pain helped to mask the emotional pain.

By this time the nanite microsurgeons had thoroughly infested his body. This is why he is called Braindead...his self-mutilation resulted in his "death"...which wasnt really a death as much as a period of dormancy while the nanites repaired the damage to his body.