Por sugestão de Vahn e confirmação do OP nos comentários, este foi O Sinal (2014 ).
De acordo com o resumo do enredo da Wikipedia para o filme:
Nic, now with the number 2.3.5.41 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...
No final:
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 2.3.5.41 (matching the numerical tattoo on his arm) that is about to dock at their home-world...