''After reading posts related to parallel worlds, multiverse theories, and dreams, I've been mulling over an idea if a sequel is made (which I do hope).
What if this game turns out to be a virtual reality experiment, designed to draw out and expand Eve's latent powers? I would assume that the "shadow organization" would have video surveillance of all of the events in the Shelter. Upon reviewing the videos, the remaining members of the organization realize that subjecting Eve to high levels of stress did not achieve the results they wanted. After seeing her interaction with Aya, they choose a more passive, subversive approach towards manipulating Eve to meet their goals: making Eve believe that her and Aya have achieved their "happily ever after" ending (similar to what the humans observed their world to be in the first "Matrix" movie). Until she met Aya, I assume Eve never had a positive experience in her life.
The kicker is Kyle, who played everyone because he still is involved with his unknown employer, the organization that is controlling everything behind the scenes. The first thing he did when he met Aya and Eve was to draw his gun on them. In subsequent encounters, he chose actions to make it seem as if he was "one of the good guys."
In reality, his true objectives are to win the trust of Eve and Aya (his actions in the Shelter indicate this), keep on eye on their movements (starting with surprising Eve and Aya at the museum), report everything to his superiors, and when the time is right, find a way to neutralize Aya and retrieve Eve. Each move he makes is calculated.
Once his objectives are accomplished, the organization creates a world real to Eve, but one that is carefully monitored by the organization, via the Overdive machine..
When I further think about it, the function of the Overdive device is similar to the helmet she wore in the Shelter--a means to control, monitor and perhaps amplify her power output. With the Overdive device, it is easier to monitor her vitals, which is something she mentions in the locker room, and determine what triggers/stressors would yield positive and negative results.
It may seem to be stretch and a bit clichéd, yet I think it might be plausible considering the circumstances.''
And another theory by him which explains all the dream stuff: http://www.gamefaqs.com/boards/951987-the-3rd-birthday/62817557