I don't think A.D. is Mary's child. Jessica would not let Mary be happy or enjoy the fact to have children. She wanted to take everything from her sister. Jessica took Charles away from Mary, she intended to do the same with Mary's second child. If Jessica was willing to put Mary in Radley each time she was pregnant, it was to be sure Mary will be on a state of disorientation (cause of electroshock and medication) and would not be able to remember every details of the birth. Jessica was pregrant too and wanted to put Mary's child to adoption. But when Jessica saw the baby girl, Alice, she felt a connection. She made the twisted choice to keep Alice and give away her own child, a baby boy named Arthur. Jessica told Mary her child died, Alice was renamed Alison, and Arthur was adopted by the Kahn family.
Years after, despite all the drugs that were given to Mary, she remembered the birth of Alice. She came back in Radley to investigate, pretending to be Jessica. It was in 2008, months before Mary's return, there was an incident on Radley's roof. Bethany Young witnessed Jessica murdered Marion Cavanaugh, Charles wasn't there. Jessica used a lame excuse (lying about an affair with her father) to get close to Bethany and bought her gift to silence her. Mary found no records on Charles' attendance in Radley, but learned that Bethany had privileges from Jessica, so she guessed Bethany could be Alice. They couldn't meet a lot into Radley, so Mary (impersonating Jessica) took her outside like in the horse stables. Bethany heard Mary's story and got mad at Jessica and all her lies.
After Jessica buried Alison, a man (Beach Hottie) contacted her and shared his thoughts about Ali's possible survival. They worked together and Jessica paid him to keep an eye on the Hastings (they know Mary and lot of Jessica's secret). This man was Wren, he dated Melissa to investigate on the Liars. Jessica kept all their discoveries in the storm cellar at Aunt Carol's house. When Charlotte had to leave Radley to become Big A, Jessica knew too. She asked for Wren's help to secure the "Cece Drake" fake identity. Wren also helped when Charlotte killed Wilden. To make sure that the cops would not tie Charlotte to the murder, they needed to frame someone else, Ashley Marin. Wren was the one who made sure Veronica Hastings couldn't defend Ashley. It's not a coincidence that Wren left Rosewood for London the same day Charlotte became the prime suspect in Wilden's murder.
Wren knew all the Jessica's secrets. He told Noel that he was Jessica's son. Jenna worked for Noel the whole time. After Toby jilted Jenna, she lost it and looked for comfort from another ex boyfriend, Noel Kahn. He shared his story with her. Their mission is to find the truth about Jessica's death. Noel sent Jenna in Welby to befriend Charlotte and used her knowledges. Noel helped to build a new identity for Archer, so Jenna could win Charlotte's trust.
Noel is one of A.D.'s helper. He uses their lair. Noel is the one who stole his own file from Jessica's lair. He took Aria's cause he investigates on her or the Montgomery family about Jessica's murder case.
I don't think Wren is A.D., he was Beach Hottie. I think he will be revealed either as Charlotte's killer or Jessica's killer. A.D. believes the killer is someone close to the Liars (Wren was close to Hanna and Spencer); A.D. is supposed to be the more clever A, maybe they haven't find the killer yet, because Charlotte's killer isn't a current Rosewood inhabitant.
Alison will be revealed as Mary's daughter in 7x10.