For those who need a refresher: We've seen the diner that Toby and Spencer (Troian Bellisario) met up at in the finale before. During the tag for Season 2, Episode 12: “Over My Dead Body” (the Season 2 summer finale), after the Liars had been framed for Ali's murder while searching for Dr. Sullivan, we saw Sullivan in the diner. She angrily told an "A" that she'd done everything "A" asked, and then walked off.
After that, the waitress in question came up to the table and said, "How are you doing tonight, pretty eyes? You want a piece of pie?"
After Mona (Janel Parrish) was revealed as "A", we filed that scene away as solved, assuming that Mona was the "pretty eyes" in question. However, in this episode we learned that the waitress calls Toby "pretty eyes."
Unless the waitress has the same nickname for two members of the "A" team, that means Toby was the one intimidating Dr. Sullivan. That would certainly explain how he was able to find Sullivan and bring her back to Rosewood in the Season 2 finale.
However, this raises several questions. First: Why did Sullivan not tell the Liars about Toby? Is she still being blackmailed? Is she really evil? Can we trust anything she's said?
Second: How long, exactly, has Toby been part of the "A" team? Based on this evidence, he's been living a double life, and doing some very shady thing, for quite a while. Is all of that pain worth it?