Dead Eyes

Dead Eyes was a series by John Smith and Lee Carter which ran in 2000 AD progs 1577 to 1588 (2008). It concerned soldier Danny Redman's quest to uncover a government conspiracy which has turned him into first a guinea pig at Porton Down, and then a fugitive. It ended with humanity being wiped out by a tribe of subterranean dwelling Neanderthals, and with Danny's death and, in a rather surprising twist, subsequent resurrection as an agent of Indigo Prime, a group who hadn't appeared in 2000 AD since 1992!