My whole theory on Requiem is probably a bit far fetched. I know there exist some theories but I might as well post my own right here. And before I begin please forgive me in advance for my bad English - being German.
So Black Plaque ended with the test of the Tuurngait. They checked on Philip wether humanity is worth to exist further. As Philip passed the test they asked him to keep their existence a secret so they can live without being wiped out by mankind - and he did exactly the opposite.
Now the events of Requiem kick in.
In the beginning you see Philip standing in front of the PC afte rhe just sent out the eMail to his friend : "Kill them. Kill them all..."
Just after that Philip is knocked out by a Tuurngait.
What I think happens is that they infected him - wanted to make him part of their hive mind (second time of course - he curec himself in Black Plaque already but I think when he was knocked out he was supposed to be "infected" again).
Now the Puzzeles you solve during the event of Requiem of course are just part of the Gameplay - giving the player something to play around with.
As for the story I think Philip slowly drifts away into part of the hive mind which is composed by the actual Tuurngait minds as well as the minds and memories of the scientists of the shelter.
This is probably why Philip visits so many areas which seem to be part of the shelter - some parts he never visited by himself but probably other scientists visited before him. Maybe he even relives stories of the other shelter inhabitants - which happened beofre Philip even entered the shelter himself.
The whole "reason" this all happens I think is that Philip struggles against the "infection" - he fights against becoming a Tuurngait. Maybe all the puzzle-solving are supposed to keep his human mind (i.e. logic) intact (of course again I think it's mostly non-symbolic but just a Gameplay element).
In the end of the game you are given the chance Red had:
Redemption by death. You can pull the switch of the funrance and beat the "infection" - by the cost of your life. (my guess: "good ending")
Or you turn around, go through the door and give in your mind to the Tuurngait hive - represented by Philip ending up on the ship again. Stuck in the infinite hole of your own and others memories inside the hive. (my guess. "bad ending")
Now what happens after that? We cannot be sure. Did Philip's friend bring the army in to wipe out the infection? Or does his friend relive the same story? We might never know...
So this is my whole take on the story. I might be totally wrong here but I think there's enough room for interpretation here, right?
