Operation Starseed - thoughts?

This is the quest with Ghengis Khan, President Franklin and the African Queen lady.

At first I was super impressed with this and really liked how it was developing. I wasn't quite following the premise but I was enjoying getting into it, with the light horror elements of the Facility.

Then I got back from the spaceship with the code or whatever it was and then for some reason had to kill Ghengis and go back to other part of the facility. .

Now, again, I liked the action and the design and the gameplay was good but it just abruptly ended and I really didn't understand what the conclusion actually was.

So even though the quest markers were gone after leaving the Facility for the second time, I went back to the place where Ghengis etc lived only to find everyone was dead, not just Ghengis but the African lady, Eva Lovelace and the President and all their followers.

Can anyone explain what exactly is going on in this quest? I felt quite let down by the lack of story clarification and the abrupt ending.