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!

Giving some more thought to this particular story of yours especially with regard the alternative future possibilities and combining that with your time travel.

What if we were to suppose the following:

The Aliens are not aliens but in actual fact descendants along the mutation timeline who have deliberately returned to create the paradox using the player that ensure their timeline is the one that eventuates. Everything would be as per the first playthrough where they present themselves as "aliens" and subsequent story follows inline with your plot.

In the second playthrough this leads you to that ultimate choice at the end do you undo the paradox by returning in time (having gained the knowledge of how to do it in the first playthrough) or do you embrace the new world i.e. inline with my earlier commentary.

The idea that a possible future might act to ensure it's existance is not a common theme. Must admit the only example I know of its use as a theme would be Jack Williamson's Legion of Time

This cuts out the element of "Aliens" persay which in some ways part of the story that rings less true to me..or perhaps that is more an interpretation of what I have read above.

Excerpt from the book:

The world is a long corridor, from the beginning of existence to the end. Events are groups in a sculptured frieze that runs endlessly along the walls. And time is a lantern carried steadily through the hall, to illuminate the groups one by one. It is the light of awareness, the subjective reality of consciousness.

“Again and again the corridor branches, for it is the museum of all that is possible. The bearer of the lantern may take one turning, or another. And always, many halls that might have been illuminated with reality are left forever in the dark…

“You, Denny Lanning,” she went on, “are destined, for a little time, to carry the lantern.

Ah, I see sunandshadow. Thanks for that heads up.

Hmmm, interesting twist, Stormynature. One I will certainly keep in mind. Thanks.