But creator I. Marlene King tells PEOPLE the story "was three and a half years in the making."
"If you go back and watch all the CeCe episodes, you can tell that we were building her A story," King says of "Big A" really being Alison (Sasha Pieterse) and Jason's (Drew Van Acker) long-lost sister, who was confined to a mental institutional as a boy named Charles and scrubbed from the DiLaurentis family tree before transitioning into Charlotte and infiltrating her siblings' lives. "She almost gives herself up on multiple occasions."
Vanessa Ray, who has played CeCe Drake since season 3 on the ABC Family mystery, tells PEOPLE she received the script revealing character's true identity in June – the same week that Jenner's Vanity Fair cover went viral.
"I felt like I was thrown right in the middle of this huge conversation, but I couldn't have it yet," says Ray, 34, of keeping the secret. "It gave me a little bit of time to sit and think about this. It was really important the way that we told this story, because it's really important that people recognize that her being transgender didn't make her A. Her being neglected and basically learning to devalue humanity, and her own humanity and her own truth, is what caused her to then devalue other humans and other life."
"Nobody would show her honest and unconditional love, that was not a part of her vocabulary, and because of it, she was able to fall down this path of just thinking of humans as dolls and not as people that have hearts and minds and souls," she continues. "It was really important that we be delicate with that."
Eric McCandless / ABC
"It just felt like the right story, so I wanted to be truthful and tell it in an honest way but also be sensitive to the transgender community, and I think we created a very well-rounded character who just happens to be transgender," she explains. "She is not A because she's transgender, she's A because she's mentally unstable and she comes from a very crazy family."
But what about the cringe-worthy fact that CeCe being Charles means Jason unknowingly dated his sister?
Let's just say that made it onto Ray's script notes.
"I would write questions that I had about the scene or a character or whatever, and the very first question I wrote was, 'Did I sleep with my brother?' " she says, laughing. "That one was weird to reconcile with. But what really made sense was that she loved her family so much and she wanted to be as close to them as possible, and the thing is she felt an instant connection with him and he felt an instant connection with her. Not because they wanted to get it on, but because they were related. When you meet your family member, the way that they move is a way that feels familiar to you, and the way that you talk feels familiar to you. So I think there was a familiarity that they felt immediately, which is why they had a relationship.
Luckily, the romance stopped short of incest.
"She kept it PG, G for sure," Ray says.
When PLL returns for the second half of season 6, the show will have jumped forward five years. King promises that the still unexplained death of Ali, Jason and CeCe's mother will be explored, and that we'll see CeCe in the first episode back.
As for the drunk mom club – Ashley Marin (Laura Leighton), Ella Montgomery (Holly Marie Combs), Veronica Hastings (Lesley Fera) and Pam Fields (Nia Peeples), who cemented their status as the worst prom chaperones ever after getting tipsy on red wine and deciding to investigate the DiLaurentis family's basement without bringing their cell phones in the penultimate episode – they're doing just fine.
"I think they're still trapped there," King deadpans. "No, they're out. That was really a time permitting thing, I wish we could have shown them getting out, but we will see them healthy and not still locked in the basement five years later."
Pretty Little Liars returns to ABC Family this winter.