The Signal (2014).
Three MIT students – Jonah, Nic, and Haley – are on a road trip to move Haley to California[...]. During their stay in a hotel, Nic and Jonah discover that a hacker named NOMAD, who nearly got them expelled for breaking into MIT servers, has found their location and is taunting them with strange and ominous e-mails. They track NOMAD to an abandoned house in the middle of Nevada and decide to go after him. After finding nothing in the house, Nic and Jonah hear Haley scream and run outside, only to see her pulled into the sky before disappearing into a white light themselves. [...]
After hitching a ride with an old lady who seems sweet yet oddly troubled, Nic and Haley hijack an 18-wheeler truck to try to find a way around the seemingly endless canyon that extends around the facility and surrounding area. At a visitors center, they come across Jonah disguised as one of the facility workers dressed in a white hazmat suit. 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 (because they both have the same tattooed number, which adds up to 51), and that this is all a test. After Nic discovers indications of alien technology also implanted in Haley's spine, the trio drive up to a military checkpoint [...].
Nic finds himself inside what appears to be a different, larger exterior facility. Housed within it, through the broken barrier, can be seen 'Area 51", the Earth-like world with the canyon city. Looking in through the hole towards the bridge, he sees Damon walk up and remove his helmet to reveal that he is actually a robotic alien, with merely a human-like face. Nic turns back around, and through the glass sees stars and outer space. He realizes he is not in a government facility, but is actually on an immense alien spacecraft numbered 126.96.36.199 (matching the numerical tattoo on his arm) that is about to dock at their home world (signaled by the horn).
Found by remembering a friend telling me about this movie a couple of years ago. I've never actually seen it myself.