1 Telly wasn't delusional
Telly wasn't delusional. She truly had a kid called Sam and all the memories that she recalls of him are true memories and not constructed ones.
2 Sam was abducted by Aliens
Sam was abducted by Aliens along with other kids. The aliens wanted to create an experiment on humans to see whether the bond between a mother and a sibling can be diminished or not.
3 Humans were working with Aliens
The humans were co-operating with the Aliens to prevent a bigger scale invasion. They thus worked with the Aliens on the experiment.
4 People's memories were wiped out
The memories of the people who knew Sam were wiped out for the sake of making the experiment. Jim's memory was also wiped to further convince Telly that she never had a child.
5 Ash had a daughter as well
Ash who was a part of the experiment had a daughter as well but he forgot about her after the Aliens wiped his memory. He remembered his daughter when Telly reminded him of her.
6 The NSA wanted to contain the situation
The NSA wanted to contain the situation not to piss off the Aliens and cause further troubles to humans. While they seemed evil in the movie their intentions were actually good.
7 The experiment failed
At the end of the movie it was clear that Telly never managed to forget about her son even after the Alien who was disguised as a man tried to wipe her memory.
8 Telly returned back to the same point
After the experiment ended Telly was returned back to the same point of time before everything started yet she didn't forget what happened. She found sam, Ash and his daughter Lauren.