For this, I thought the fact that going back in time and having him actually be the one that started the plague, even though he was trying to stop it, was the unforeseen consequence.Am I wrong on that?
Essentially you are creating a paradox with this thought i.e. the destroyed world he wakes to is the result of a future action of his. This can open up themes revolving around fixed causal determination, free will, multiple worlds theory (resulting from changed decisions) etc.
One way in which you might play 2 run-throughs is in the first playthrough the uninfectected human views the current devastation of the world through the eyes of horror, whereas on the second playthrough using the mutated cancerous state you start seeing the changes through a different perspective i.e. has humanity necessarily died out? or evolved into something incredibly different which you being infected can now connect to, leading to the determination of whether this "new" form of existence (while vastly different) is something to embrace or must you race back in time again to attempt a further change.
I love that idea. That sounds incredibly fun. I need to see if I can work that concept into the overall story in a natural way. Thanks!