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.