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Now that Julia has discovered the hedge witches who live in New York City, she starts to learn their magic – which they keep in a large binder of spells they have collected and put together and generally keep under wraps. Meanwhile, Dean Fogg has been growing new hands and has big, crazy, fake eyes that he can't see out of AND he has a series of announcements. Going forward, each of the students will specialize in a specific type of magic, which is pretty standard practice at Brakebills, just it's going to come a little sooner than usual. Thing is, if you start messing around with magic you don't know enough about, you could hurt yourself or someone else.
So, everyone is examined by various professors to find their magic specialty. Alice's specialty turns out to be phosphoromancy, which means she can bend light. Penny's specialty is just boring old psychic ability and Quentin's specialty is, well, he doesn't have one. Either way Alice and Quentin are sent to live with the "Physical Kids" – those who do physical magic and live in the "physical cottage." In order to get into the cottage, Alice and Quentin have to magic their way in. They pull it off by bending light and then get drunk and Alice confesses that she wants to retry the spell that brought them The Beast – because ultimately what they were TRYING to do was conjure her brother Charlie.
The search for Charlie's spirit leads them to the fountain where Charlie died, and something about their being there brings an evil spirit (Charlie?) out of the water to secretly drown a few students. Quentin and Alice want to learn more, but Eliot interrupts and pulls Quentin away to find the book that Kady stole from the physical cottage. Alice, meanwhile, is left to ask Margo what she knows about Charlie's death.
It turns out that back when Charlie was at Brakebills, he helped a student named Emily Greenstreet, so Margo and Alice head off to find her. Emily wants nothing to do with them but tells them the story: she tried to make herself more beautiful, messed up her face by using a spell, and Charlie tried to help her. In the process, Charlie's magic got away from him and he made himself into a niffin: a blue fire-ghost basically.
Eliot and Quentin use the second edition of the missing book to find the first edition. See, at Brakebills, the books like each other quite a bit, and are downright amorous, so a missing book is best located by taking its mate out for a walk. That search leads Quentin and Eliot right to Julia and the hedge witches. It doesn't go great because Quentin and Julia have been needing to clear the air: he calls her out for always knowing that he was in love with her and she is angry that he wouldn't help her get into Brakebills. Quentin tells her that she's just angry that she wasn't good enough to get in. So. Friendship over.
When Penny drops in on the attic to meet the other psychics, he finds out that he's not a psychic at all when he somehow transports himself to China. Penny turns out to be a traveler – someone who can, theoretically, move between worlds. From now on, he's going to be studying with Professor Sunderland one on one. Meanwhile, you know who's having a hard time holding everything together? Julia. All the hedge witches tell her that she has to manage her personal life. So she lies and tells James that she's on drugs as an excuse for her weird behavior lately.
Quentin warns Alice of all the ways that bringing Charlie back is dangerous, and as a precaution brings a "niffin box" to her spellcasting (against Alice's wishes). When Charlie reveals to be a little bit evil and out of control, Quentin traps him in the niffin box, ruining any chance of her bringing him back for good and also ruining his relationship with Alice, whose hope is lost for good. Alice is furious, packs up, and leaves Brakebills for good.