So, I know what a lot of you guys are thinking. A.D is a guy! It was confirmed in the flash forward at the end of 6X10. Well, my good friend, not entirely! From what we have seen from the previews of season 7 and from what we know of season 6b, they "He" chasing Ali is, in fact, Dr. Elliot Rollins. He is manipulating and abusing Alison to make sure he controls the Carissimi Group. The Liars will eventually realise this and attempt to save Alison from Dr. Rollins and Mary, leading to some big climax. That flash forward was to trick us into thinking that Uber A is a man when, in fact, it could be a woman.
Now after I have cleared that up, I want to delve into the origin of Maya St. Germain or A.D. Maya was born to Mary Drake and Eddie Lamb. Mary was admitted to Radley, where she met a young student nurse named Eddie. The pair fell in love and had a romantic relationship, which resulted in Mary getting pregnant. Mary and Eddie didn't want anyone to find out because Eddie could loose his job and they wouldn't be allowed to see each again, so she had her daughter Maya in secret. Maya was given to Eddie's sister (who couldn't have children) and this allowed him to keep an eye on his daughter as she grew up! With both of her children gone, Mary became bitter and her relationship with Eddie ended after they were caught by Charles, who told Jessica, who was on the board. Jessica warned Eddie to stay away from her vulnerable sister or he would loose his job. Mary then became hateful towards Jessica. Her mental state allowed her to believe that Jessica was the reason behind her loosing her children, being locked up in Radley and she hated Jessica for having a perfect family with a perfect husband.(This later fueled Mary's revenge when she killed Jessica).
However, a few years later, Maya and her adoptive parents moved to Rosewood in an attempt to tell her about her real family. The st. Germaines had hoped that when they confused about Maya being adopted and that her biological parents resided in Radley, that it would be easier for her to communicate with them.But Maya's drug habit had gotten in the way and her parents had to get her stable before she could find out about her past.
When Charles transitioned into Charlotte, she began to search her family and she went to Eddie about "Maya". Charlotte blackmailed Eddie into telling her and she tracked her down and they had a close relationship. Charlotte told Maya all about her family and what happened between Eddie and Mary, which shocked Maya to her core. It also contributed to her relapse and sent her to True North. There, Maya met Landon, who stalked her and harrassed her. In an attempt to help her sister, Charlotte helped Maya fake her death live out a free life with her mother, Mary, who was also out of the country. Maya willingly did so, always accepting that she owed her sister.
When Charlotte went to France, it was to see Mary and Maya. Mary had just killed Jessica and was having a psychotic episode and Maya needed help. Once again, Maya owed her sister.
Charlotte and Wren were friends,so she told Wren about Mary and Eddie and how he gave away Mary's baby! Wren was distraught over this and, due to issues with his own father, teased Eddie and threated him everytime he questioned Wren's illegal activities as a doctor. When Eddie seen Aria that day in Radley, he thought it was Mary coming back for him. He had always loved her and Maya, but he couldn't go to jail and loose his job. (Mary was a vulnerable patient, it could be seen as rape).
When Charlotte was murdered, Maya knew it was the perfect opportunity to avenge her sister after everything she did for her. She is A.D (After Death) because it was Charlotte's game and she wants to bring her killer to justice.
I have a feeling that "Mary had a little lamb" comes into play here. Mary had a little lamb (Maya Lamb(Eddie's child)) who's fleece was white as snow (Maybe this refers to the wool cap in her bag that she ran away with (a gift from either Eddie or Mary))/ everywhere Mary went,the lamb would surely go (When Mary was at the Lostwood's Restort, so was Maya and she kidnapped Hanna)
Also, the photo of Alison and Shanna was actually Ali and Maya, who visited Ali sometimes, but neither remember.
"MAYA KNEW" was about Charlotte telling Maya about the diaries and what she and Alison did. Maya also visited Charlotte a couple of times when Mona was in Radley. Maya knew the -A game was starting again and wanted to help her sister, but wasn't revealed because Charlotte was protecting her again.
"Lord help the mister who comes between me and my sister"- refers to Landon trying to kill Maya/ Wilden tracking Alison (who was her best friend)
If you have any questions, just ask and I will try to respond to them as best I can!! :)
I dont support this theory but i see how maya could be alive. She was attacked by Lyndon and he thought he killed her but Big A found her unconscious and barely alive and gave her that stuff that made Mona, Kenneth and Jason seem dead. Maya would stay this way until after she was identified but her body was swapped for someone else's before dissection