That sort of Re-Take of Madoka is too pedestrian to be the Master's handiwork. Nor, alas, would be the Gurren Lagann ending.
Nor would be the"all in Shinji's head" interpretation currently being circulated on /a/
After 3 years Shinji gets released from a facility, where his Teacher tried to get him to cope with the loss of his mother.
He telephones his father in Tokio-3, but his father refuses to answer the phone. Cue first angel attack. Shinji lapses in and out of psychosis, with Misato's apartment, the school and the hospital more likely to be reality. Each time Shinji is spurned, disappointed, threatened, or underpressure an angel attacks.
"THIS IS THE STRONGEST REJECTION TYPE ANGEL YET."
So no, NERV HQ doesn't exist. And Yui is _dead_ dead.
Some middle aged Fujoshi picks him up on the street in a sports car. (Also, she works with his father). Bits are real, bits aren't, but they're all part of Shinji's delusional state and mental illness. The giant robot battles directly equate to his adolescent angst. So Gendou probably does run a large organisation, but it probably _doesn't_ use giant fighting robots to save the world. Unless Shinji actually is really summoning Angels while being fucked in the head. Occams says that he probably isn't. Occams says that Rei is just a spooky girl who lives alone, and then rejects him for some unknown reason when he refuses to save her from the Gendou rape train
It depends on who is a delusional fantasy entirely, and who is merely Shinji's projection of a "real person."
We have reason to believe that Gendou, Asuka, the School Kids, Rei II/III, Misato and Kaji are _really_ real—.
However, other characters may be fully delusional— Fuyutsuki, Yui, Ritsuko, Bridge Bunnies, Kaworu—, all these characters only appear inside the "NERV" delusion, Shinji doesn't see them separately. (Yes I'd need to rewatch for Ritsuko in hospital sequences.) These characters never existed outside of Shinji's fantasy world of giant robots, where his father has an excuse not to love him by saving the world, where Shinji is important, and where his mother isn't actually dead but still loves him.
What it will involve is plenty of flying battleships, now he's gone full Miyazaki.