Charles is Bethany, Cece is A:
Okay so I’ve held off for a while on writing my own theory about Charles being transgender, mostly because I couldn’t fit the pieces together and wanted to make sure that I was being respectful, so here are my thoughts finally after the answers from this episode.
As a child, Charles never felt comfortable in his own skin. Deep down, even when he was very young, he knew that he didn’t feel right as a boy. In Welcome to the Dollhouse we found out that Jason is around 7 years older than Ali, and Charles is just over a year older than Jason, so 8 years older. Therefore he tried to kill Ali when she was 1 and he was around 9 years old, certainly old enough to be at least semi-aware of his feelings, even if he couldn’t identify things perfectly at the time.
He resented her from the moment she was born because she was free to grow up as a girl and be treated as a girl, while he felt trapped in a body that wasn’t right for him.
After this attempt, he was institutionalized. Mr. D clearly thought he was a nuisance and a danger and probably didn’t visit or care much for his son. Mrs. D chose for the family to move to Rosewood and got a position on the board so she could be close to her son.
Charles grew up in Radley, and at some point confided in his mother about his true feelings as he came to terms with them. At that time, he was 16 years old and Ali was 7.
This brings us to the flashback Ali had in the Christmas episode, when she looked to be around 7. She found two yellow dresses. I think that Mrs. D was planning on bringing the second yellow dress to Charles. Not for him to wear, he was obviously too old for that, but as a way of telling him the good news that she would be helping him get a surgery to change his gender, showing him that he could be like Ali after all. She made sure Ali wouldn’t tell Mr. D about the dress, because he would never understand what she was doing. That’s when she and Charles faked his death.
She took him out of Radley and made him promise to never reveal himself to anyone ever. She took him to Aunt Carol’s house after the surgery (maybe she knew the truth since she was visiting him too). Once he became a female, they made a grave for Charles DiLaurentis, his old identity, and he changed his name to Bethany Young. He was still very troubled so she brought Charles (now Bethany) back to Radley.
That’s why Mrs. D made the effort to bond with Bethany and take her out places. She told Bethany to call her Aunt Jessie at the stables, which angered Bethany because she knew that Mrs. D was her mother. Mrs. D covered for Marion’s murder because Bethany did it, and if it went to the cops that it was a murder, they would investigate Bethany and the truth about Charles would come out. So she paid Wilden to fake the report and make it a suicide.
The night of Ali’s disappearance:
Bethany/Charles escaped from Radley and was lured in the yellow top to Ali’s back yard. Mrs. D was called and notified because it was her son/daughter, and she was concerned because Bethany as Charles had tried to kill Ali before and still resented her for living the free and happy life that Bethany should have had too. Bethany was murdered and buried in Ali’s place, and most likely the liars did something to result in her death that they repressed due to the drugs Ali gave them, which is why A is targeting them.
So who is A if Charles/Bethany is dead?
Cece Drake. In the promo for 6x05, we find out that a female character was in Radley as a child and knew Charles. I think it’s Cece. She was institutionalized when she was younger and fell in love with Charles, not knowing about the fact that he was transgendered. Despite being told not to tell anyone, Bethany told Cece the truth because of how close they were. Cece continued to visit her, and was in Ali’s back yard that night to look out for her. She still mourned the loss of the Charles DiLaurentis that she once loved, so after the gender change, Cece changed her name from whatever it once was to Cece Drake, giving herself Charles’ initials.
Now she is acting as A to get revenge on Ali and the liars for Charles’ murder.
For those of you who insist that Marlene said that Charles is A, she may be twisting the truth. Cece, in a way, has taken on Charles’ name. She believes that she is doing this for or as Charles, and therefore in a way he is A.