Since the story wasn't continued, we don't have a concrete answer, but I think the idea is that at the end of their fake space journey, they'd actually end up on the other planet. Let me back up and explain how.
The secret goal of the Ascension project was to breed children with superpowers. Specifically the powers we see manifest in Christa. The ability to teleport people and objects interstellar distances. In Christa they found their first success.
Given the length of Ascension's planned voyage, the people secretly running it could then prepare to have the fake ship (alternatively they could build another ship which was actually spaceflight-capable, and then swap that in place of the fake ship) teleported to the planet the people aboard believed they were heading to.
Then the people aboard would be none the wiser. They'd land on the planet and begin the colonizing process. Meanwhile the people on Earth would have the ability to colonize the stars within a generation.