Near the end of Oblivion when Jack is having flashbacks to being an astronaut. He remembers piloting the spacecraft towards the alien ship. My understanding was that Jack and Victoria were both asleep in the pods, and that mission control awoke them when intercepting the unknown artifact (the alien ship).
While on route to intercept the artifact Jack is in constant contact with mission control. The woman in the video screen is the same as the woman seen earlier in the film. So it seems that Jack was following orders made by the alien, and not actually mission control.
My question is who woke up Jack and Victoria? Were they awoken by the alien and tricked into thinking they were communicating with mission control. Or, was the woman on the screen a real person back in mission control and not the alien?