Per Vahn's suggestion and the OP's confirmation in comments, this was The Signal (2014).
According to Wikipedia's plot summary for the film:
Nic, now with the number 126.96.36.199 tattooed on his arm, wakes up in a
strange and sterile underground research facility where he is
questioned by Dr. Wallace Damon, the head of the "transition group" in
charge of helping Nic to cope with his strange situation...
Jonah reveals that he too had limbs taken from him, as
his forearms and hands have been replaced with the same alien
technology as Nic's legs. Jonah speculates that they are in Area 51
and that this is all a test...
At the end:
Nic finds himself inside what appears to be a different facility
behind a projected image of the outside world beyond the canyon.
Turning back toward the bridge, he sees Damon remove his helmet to
reveal that he is actually a robotic alien. Nic walks towards a window
and realizes he is not in a facility, but is on an immense alien
spacecraft numbered 188.8.131.52 (matching the numerical tattoo on his
arm) that is about to dock at their home-world...