about the end

[Thaliur]

You can be killed by something not visible. High Energy UV rays or similar phenomena

Anyway, the Tuurngait hive mind would be able to get Philip killed, sooner or later, just by making him not see a hole in the floor, by making him forget to breathe, by making him run headlong into any kind of danger they want...
Letting the "drones" attack him would be a pretty lame option for something like the hive mind.

Something else just came into my mind...
The Hive seemed quite cooperative most of the time, at least during the trials. Constantly giving hints on ho to complete them.
Despite that, the drones kept attacking Philip. Why did they do that if the Hive just wanted to test him and get him to help the Tuurngait keep humans out of their domain?

My guess is that Philip got infected as soon as he entered the water cave (the "cave from conversations past" in Overture) and got close to the glowing material. From then on, he had Clarence sitting inside him, just as a small silent "passenger", but present.
But the Hive felt his presence, and knew that Clarence is a sepoerate entity, not part of the Tuurngait collective (I keep falling back to Borg terminology, sorry about that, it just fits so well).
So, all the time Philip was running around in the Shelter, the Hive never actually attacked Philip himself, but Clarence, trying to either kill him, or get him to leave. As soon as Clarence was seperated from Philip, the drones went after Clarence, and just watched Philip while the Hive made him complete the trials.

Anyway, back to topic:
I believe Philip managed to send the email to "us", as we are reading it while playing the game, but afterwards something unknown happened. The disappearing walls led me to believe that the Hive was, indeed, not amused by Philips (presumedly successful) attempt to betray them, and so got him killed in some way.
We, of course, don't know that, because we're only reading his email, telling us about what happened to him.