Mrs. D was Bethany’s nurse at Radley. Mrs. D and Bethany’s dad were having an affair. Both of these were revealed in 5x12 via Bethany’s recordings and personal files at Radley.
The affair between Mrs. D and Mr. Young is what lead Mrs. D to give Bethany luxuries such as signing her out of Radley and taking Bethany horse riding.
Mrs. D thought that pleasing Bethany would in return impress Bethany’s dad, which ultimately made the relationship between Mrs. D and Mr. Young much stronger. I guess you could say Mrs. D was sucking up to Bethany’s dad.
However, Alison knew about the affair between her mother and Bethany’s father. This affair upset her, as it could potentially lead to the destruction of her own family between her own parents, Kenneth and Jessica.
To protect her family, Ali needed to stop the affair between Mrs. D and Bethany’s dad. To do this, Ali needed Bethany dead, with Mrs. D at fault for the murder of Bethany.
The affair between Bethany’s dad and Mrs. D would instantly end if Bethany’s dad found out that his lover killed his precious daughter. This is what Ali wanted; the affair to end and Bethany being killed is the solution that Alison wanted to take.
Ali lured Bethany to Rosewood that night to kill her to end the affair. It all backfired when somehow, Bethany figured out the real reason Alison lured her to Rosewood - to kill her, so Bethany thought she would get one step ahead of Alison and kill her first:
Bethany threw the rock at Alison’s head, knocking her out. Mrs. D saw Bethany knock out Alison so she buried Alison to keep it even with Bethany - Mrs. D accidentally pushed/killed Toby’s mother at Radley and Bethany saw it, now Bethany (nearly) killed Ali and Mrs. D saw. They both agreed to never speak of these incidents again if Mrs. D covers up for Bethany, closing the deal and securing safety for both of them.
Whilst Mrs. D was burying Alison, we know she was repeatedly saying "what have you done!?" This was expressed to Bethany, as Mrs. D had no idea why Bethany did that to Ali, but Bethany could later explain to Mrs. D that Alison started it and was about to kill her, so it was out of defense.
Later, Alison was pulled out of the ground by Mrs. Grunwald and Mona saved her, convincing her to run away and not return to Rosewood. Right before Alison ran away from Rosewood, she had one last thing to take care of - to get revenge on Bethany for (nearly) killing her. Alison killed Bethany for revenge and left her by an open grave. Then, as revealed in 5x11, Melissa buried Bethany as she thought she was protecting Spencer for killing her, but instead it was Ali.
It was revealed in 5x06 that A killed Mrs. D.
It was implied via the black hoodie in 5x12 that A killed Mona.
Why were Mrs. D and Mona both killed by A? Because they both knew about the affair!
A does not want anyone knowing about the affair. Who can we think of that doesn’t want anyone knowing about the affair? Alison! Because the affair is what gave Alison motive to want Bethany dead, and if anyone were to find out about the affair, it could potentially lead to Alison getting years in jail, if not a life sentence, for killing Bethany which ultimately started a murder cycle. Besides, remember in 5x12 when Paige told the girls that she followed Alison, driven by Cindy and Mindy, to an abandoned farm? Alison was visiting the horse place where Spencer and Emily went in 5x08. Alison wanted to speak with Declan, the farm owner, to see what he told Spencer and Emily about Bethany and Mrs. D, who visited the farm often… and whether or not Spencer and Emily were getting closer to uncovering info about the affair.
Alison is A and is killing anyone who finds out about this affair. Alison is A and is torturing Aria, Hanna, Spencer and Emily because they are the only ones who are so dedicated to figuring out what happened that crazy night - and so by torturing them with other stuff as A, they are kept busy and are being distracted, luring them away from the affair. All of that, combined with Alison’s mental disorder of taking pleasure in torturing others, is perfect motive to be A. She assembled the perfect group to play a sociopath game on and will kill anyone who finds out about the affair as if the news of the affair gets out, she herself gets in trouble.
I feel like all evidence that points away from Alison being A, is just her trying to make herself not seem like a suspect to the other girls because lets not forget, A said that if Alison leaves Rosewood, A will kill her, yet in 5x11, Alison left Rosewood and nothing happened… Also in that same episode where Alison left Rosewood, we never saw a typical A ending scene at the end of that episode! Because A/Alison was out of town. And in 5x06 when A strangeled Ali… A had such an easy chance to kill her but didn’t! All Ali needed was one scratch or choke mark on her to scare the other girls and make them think that A is after her too, when really, it was all planned and under the hoodie could have been Cindy or Mindy! Fortunately for Ali, Emily walked in on the performance staged by Ali, giving Emily a real experience instead of just hearing about a story to make Ali not seem like an A suspect.
Well, that’s where I feel Pretty Little Liars is heading! Of course there are probably some holes in this, as A is the hardest character to analyze. What do you all think about this affair being a major turning point?