At the end of Penumbra: Oveture what is the thing that takes you away?

[Adny]

Either it's never truly explained or I just didn't pick up on it. The only thing I can think of aside from the generic "experimentation", would be that the enemy is aware that Howard is your father (who is one of the only people that can talk to the Tuurngait), but that wouldn't explain the other prisoner.