Since 6B, we saw interviews about Big Bad a.k.a. Uber A a.k.a. A.D. Marlene said it will be the smartest A, the most driven to win the game, A.D.’s revelation will blown the others out of the water.
First, I dislike the idea that the term Uber means that this A was the master of Charlotte or/and Mona.
The 3 A had 3 different stories, but I do think they interacted a lot.
Second, I feel like love and family could be part of the motive. It’s how Marlene build her villains.
And finally, I believe AD isn’t the biggest mastermind but more like one piece of a complex final story to take place in the last episodes.
Now the actual theory:
What happened with the Drake twins ?
From flashback in episode 7x07, it seems that Mary was back in Rosewood during season 3. After the confrontation between Jessica and Mary at aunt Carol’s house, I think Mary decided to stay around.
We saw Mary Drake once, before season 6. I believe it was in episode 4x22 when "Mrs D" appeared in Spencer’s room. Since Mary thought Charles was dead, she wanted to see the child born from her egg implanted on Mrs Hastings (in this theory, Mary isn't a surrogate, but the Hastings used Mary's egg to have another child). But Veronica found out that Mary was in town and got scared.
Remember the drunk mom scenes from 6x10. On the right pressure (and with help of some wine), Mrs Hastings can lose her temper and act in the heat of the moment. Spencer’s life was such a mess at this moment (the addiction), Spencer surely didn’t need to find out Veronica wasn’t her biologic mom (despite being the one who gave her birth and raised her). Veronica used the medication to knock out Mary, but it had too strong effect on her and she died.
That same night, Jessica came back from the police station. She was convinced Alison will soon be back and people could find what she did the night Ali disappeared (she buried her to protect a secret child hid in Radley). Then she saw Mary’s dead corpse. Too stay hidden in Rosewood, Mary used to wear same clothes as Jessica. Jessica thought that it was the perfect occasion to start over. People would assume Mary was Jessica, so the real Jessica could disappear. However, before leaving, Jessica found a clue that prove Veronica was guilty of the murder. Jessica left town, to come back only five years later, pretending to be Mary.
PS: the twins ghost little girls (from 3x13) was foreshadowing to the story of Mary and Jessica Drake. One twin died, the ghost told Ashley that her sister was the bad twin (Jessica, the one who is still alive).
Why AD want to find Charlotte’s killer ?
Someone was talking with Charlotte when she was in Welby, using letters signed AD.
It was Jessica, pretending to be Mary. For some strange reasons, Jessica felt closer to Charlotte than to Ali. AD is for Alice Drake, Alice was Mary’s second name.
Thanks to passports found by Spencer and Toby, we know that Jessica came in town one week before Charlotte’s release. After Charlotte’s death, Jessica was desperate to find what happened, and when she saw Melissa back in town, she confronted her. Melissa wasn’t the killer, but Jessica wasn’t ready to leave her out of this.
She shared with Melissa that she knows her mother killed Mary. How awful it would be if this information was leaked during Mrs Hastings’ election compaign. Melissa became Amoji because of the blackmailed from Jessica. (Marlene said Uber A was the smartest, it doesn’t mean this A can’t be manipulated or can’t act for someone else. Both Spencer and Mona are smart, but they were often fooled by other people through the series.)
Melissa hated Charlotte. She doesn’t care about the killer, but Jessica does. Melissa’s motive was first to protect her mother.
Amoji sent this "I guess she is better than you. He will never put a ring on your finger" to Spencer. It looks like something Melissa could tell to her sister.
Melissa loves the competition, she is the kind of character who would be really driven to win the game !
Veronica's campaign was a huge deal in 6B. Uber A really wanted the girls to find answers before the results. After Veronica's victory, the initials A.D appeared. (for Mary A. Drake, the woman killed by Mrs Hastings, as a reminder of a sinister and unforgetable past for Melissa)
There is (according to Marlene) one question that hasn't been really asked yet http://screenertv.com/television/pretty-little-liars-last-10-episodes-more-weddings-flash-forward/ . I saw here and on various others forums a lot of questions/theories about AD, the killer, Charles, Bethany... but there is one plot detail that a lot of people don't talk about anymore. Even in the show it's a storyline they left unfinished. Who's blackmailed Melissa with her confession tape. In 6x18, Peter told Spercer that Melissa was a victim and that she had to give that person lot of money so her confession about bethany will stay secret. We all know how Spencer found Melissa killed Bethany. By a tape Spencer destroyed right after. There is no way somone else knew about this tape. So I'm calling it, it was a lie. Melissa was never blackmailed about her confession. She uesd this money to finance her AD stuff !
Hanna’s dream from 7x01: Melissa is Spencer's sister, it's probably easy to her to mimic Spencer's gesture. Hanna was tired and maybe druged, so she didn't notice that person wore a Spencer's mask.
Rumor about Alison’s pregnancy started by AD: if Melissa is Uber A, clearly finding the killer isn’t her main goal anymore. She plays with the Liars. The A game and Alison’s lies cost Melissa the death of two babies. A twisted revenge would be to make Ali live the same experience.
Full Circle: The show started by the discovery of the body believed to be Alison. If Melissa never buried Bethany, people would have never assume Ali was gone for good and Mona wouldn’t have been able to trick the girls with Alison’s style messages. Melissa’s actions started and will end the show.
What about Noel, Jenna and Sara ?:
Jessica never told to Charlotte that she was alive and Mary was the dead one. Jessica always posed as Mary Drake (or AD in her letters). But Charlotte was suspicious of something. She used Jenna to investigate on "Mary". In 7x07, Caleb found a DNA test. Jenna and Noel wanted to know which Drake was in town.
In 7x10, they abduted Jessica into this old blind school.
Jenna shared their informations with Sara; which scared her. She was really afraid of Mrs D, and thought she was free of her since her murder. Cause Jessica is the one who abducted Sara the day after Ali disappeared (Sara was really Sara, not Bethany. Everything about Sara was true, expect Charles was never her kidnapper). In 7x06, Sara tried to warn Emily about Jessica faking to be Mary, but Jenna stopped her cause she doesn’t trust the Liars or care about their safety. Jessica killed Sara in this same episode.
Everything related to the night Charlotte went to the bell tower:
A few people were there that night. Ali, Mona, then Lucas. Mona had a violent fight against Charlotte and hit her. Lucas arrived at this moment (he had a secret meeting with Charlotte). He helped Mona with this "muder". Mona had the idea to stage the scene, using details from Spencer criminology essay. She left to take some stuff. That’s when Lucas noticed Charlotte wasn’t dead indeed, just unconscious. Lucas took Charlotte away.
Melissa have two big helpers beside Jessica: Wren and Lucas. Wren provides the medical experience, and Lucas provides the mask knowledge and some spying on the girls from the surveillance tech on his apartment.
Wren was always on Charlotte’s side. He will have surprising twists when he will reveal that Charlotte is alive but imprisoned by Lucas, and when he will take the fall for Mary’s murder to protect the Hastings as a proof of his love for Spencer. (Marlene said Wren will return in a positive way)
Jessica hates Ali for unknown reasons. During the first seasons, she knew Alison was still alive but never made her come back. Now she's impersonating Mary and doesn't want to reveal herself to Ali. Jessica will be the true ultimate villain.