What was the contagion? What disease did the three of them have, that the other humans didn't?
They didn't have any disease. Initially, they were sick with the extreme limb transplants and mind experiments. All the talk about the contagion was a ruse to keep them in quarantine. later when they are out of the underground facility, Damon wants them to think like escapees. Also, Damon and his team had to hide their robotic identity and appear like human doctors/lab workers.
Why does Haley hear the sound but not Nic?
Maybe she was used like a transponder to track Nic and Jonah. We see some device attached to her spine.
Why shoot them? Surely someone with such slick tech doesn't need to kill someone with a gun. Why blow them up?
The same reason why lab animals are put down when they get out of the cage and become a threat to the people who are testing them. That explains why Damon and his team approach Nic with caution from the get go.
Then I wondered -- who are the aliens?
Is the Doctor an alien or a tool of the Aliens?
And I wonder about that because -- why bother use a human face?
Why not just have a talking suit? Why do the other lab workers appear human?
Why be humanoid at all?
We never know who the real aliens are. Damon looked like a sentient robot designed by the Aliens to run these simulations. The human face and earth-lab like environment were essential to make the subjects feel at home and not have a nervous breakdown during the simulation.
And if they're just meat, to be experimented with at will, why go through the whole attack on MIT
lure you out to the desert bit at all? Why not just go to MIT and beam up a few students? And what was The Signal? It seems it took a series of events, and elaborate wriggling lure of internet attacks and incursions to get their attention and involvement -- not a
"signal".
I think he was talking about the first signal from "Nomad". Nic and Jonah think that it is a message from the hacker who got them in trouble.
Luring them was necessary to make them feel that they are still on Earth( somewhere in area 51) talking to human doctors. Also, it was a test to see how intelligent and motivated they are. When the Aliens see that these three people are smart enough to trace the signal to its physical address, they abduct them. As Damon says in the end, the purpose of the experiment was to see what happens when human will meets Alien technology.
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