I think the apparition is the spirit of that black mage in disguise. The prophet "survived" in the dream world, why shouldn't the black mage. Another theory of mine was: That the "prophet" we encounter in the dream world was actually the apparition. The MC is fooled into gathering the shards and bring them to the dream world. As for the dad. I think he is simply held hostage in the dream world, but in order to ensure a harem ending he will probably not survive it. As for Alice, since she asked for the MCs computer password "to play games" I can't shake the feeling she is working for the order, probably forced or unknowingly.
I agree about Alice, however i'd hazard that if Alice is a tool of the order then so is Aby and quite likely so is Aunt Jenna.
As for the Apparition being the old enemy to borrow a phrase this has potential, we don't see the Apparition in the flashbacks and he does come off as sinister not to mention he is holding back plenty of information. It's also telling that we don't see him and the prophet in the same scene although the prophet does seem to have an idea that the MC has a certain amount of experience with the spell and the way the dreamscape works, as such i'm not sure if the prophet and the apparition know about the others involvement with the MC or not, if not i can see the MC having to choose between them.
We have far less info on the Dad, simply that he is ill and out of the picture presumably due to the order and as such is leverage against the MC. As to if dad survives i agree with you that his chances aren't great due to the Harem ending, i wonder however if he'll play more of a role in the finale or just stay as a passive background element.
this does lead me to think that with the cast we have the MC is becoming outnumbered with very few people to count on, i'd divide them up as follows:
Mrs Turner - on the MC's side and oblivious to the goings on thus far
Tracy - probably the only real ally the MC has at this point that he can trust
Alice - presumably under the control of Nora and the order, unwilling against the MC
Aby - presumably on the same side as Alice, either unwittingly, intentionally or through mind control working for the order
Aunt Jenna - Quite possibly on the side of the order via mind control, that or unwitting and therefore a potential ally to the MC
Nora: against, i'll count her, the demon and henchman as one for simplicity sake
Apparition - presumed against the MC, although he may simply want the shards back to rule the dream world, leaving the MC to his fun in the real world
Dad - on the side of the MC by way of the fact that he's taken out of the picture presumably by the order
this gives a score of:
in favour of the MC - 2, Tracy and the MC, yeah slim picking here at best
Nora: 1 + up to two presumed controlled family members and Aby, not to mention henchman and a demon, the only legitimate threat to the apparition that i can think of so far
neutral/unwitting: Mrs turner and perhaps Aunt Jenna
so yeah with those numbers i don't see how the MC is getting out of this one, there is Markus to consider although i doubt he will be worth much beyond what he has already done