Were they ever actually on earth?
This is one of those movies like Donnie Darko that has many possible interpretations, and probably by design no absolute right one. My own feeling after watching the end is that our characters were not human subjects being experimented on and made into alien machines, they were alien machines trying to make themselves human. In other words Nic and his friends didn't live the lives they remember. All memory from before the experiment/project/whatever you want to call it, is a fabrication. The world outside the "game zone" was never actually there for them to reach.
Perhaps the ship at the end is an alien vessel that's arrived near earth with either a race of machines or a single hive consciousness on board, which for some reason wants to become more like us. Or it could be one of ours. If faster than light travel is impossible, and putting bodies in cryo-suspension for thousands of years won't work either, then maybe the crew would download their minds into the main computer to survive the trip. Over time their humanity and even their individuality could be lost. Now at their destination they're figuring out how to get it all back. Nic and Haley could be two people who once loved each other, struggling to remember themselves and be together again. In which case some of those old memories may not be fabricated after all.
Or how about this one? A wandering machine intelligence called Nomad finds earth some time after a disaster that wiped out all life. Because even the bacteria are gone human bodies not directly exposed to wind or water won't break down. Nomad (a.k.a. Damon) tries resurrecting our species from preserved remains as best it can, to give us a second chance.