Moments after where the season five finale left off, Aria, Emily, Hanna, Spencer and Mona are trapped outside of Charles’ Dollhouse with nowhere to go and must now deal with an angry tormentor. Just when the Liars thought Charles couldn’t get any worse, his games take a more demented and darker turn. As the girls struggle to survive, the puzzle of Charles’ story begins to come together. Meanwhile, Ezra, Caleb and Toby continue the fight to find the girls with or without Rosewood P.D.’s help.

It is prom time at Rosewood High School, except for Alison, Aria, Emily, Hanna and Spencer who have been banned due to "security" concerns. As the girls see this as the final humiliating blow to their high school careers, the girls' mothers try to make the best of a bad situation by offering a home prom in Spencer's barn. At first reluctant, the PLLs agree and try to make the best out of a bad situation. But one to never miss a formal, Charles has other plans in store to make this a night they will never forget. Meanwhile, Veronica, Pam, Ashley and Ella use prom night to touch base on everything that has happened to their daughters.

There are mixed emotions in the DiLaurentis household when Charles declares he is coming home for his birthday. Mr. DiLaurentis wants to quickly get out of town to hide Ali and Jason from their brother, while Jason sees this as an opportunity to finally validate all of the early childhood memories he has of “Charlie.” The PLLs are just as split with Spencer and Hanna seeing this as the best chance they have to capture Charles, while Emily and Aria want to stay as far from him as possible. Will Jason be reunited with his brother, or is this just another of “A’s” traps? Meanwhile, Mona is shutting Mike out and Hanna gets an unwelcomed surprise.

After their latest run-in with Charles, tensions are at an all-time high with the PLLs and the town of Rosewood. Aria’s big moment of seeing her work displayed in an art gallery is in jeopardy as Ella is determined to keep her safe at home. Hanna is still uncomfortable with the unexpected scholarship money and is determined to give it back, even if that means ruining her chances at going to her school of choice. And to top it off, the one normal high-school rite of passage the girls are looking forward to is in danger as Rosewood High is considering not letting the PLLs attend prom due to security issues. Meanwhile, the more Alison learns about her brother the harder she finds it to connect a deranged murderer to the young blonde haired boy she sees in the photos and in her memories.

The girls may have gotten out of the Dollhouse but what happened to them during their time of captivity has lasting effects. With worried loved ones watching over them, the PLLs are home and trying to heal, with not much success. Even with suspected tormentor Andrew in custody, Aria, Emily, Hanna and Spencer fear they are far from safe. Meanwhile, Alison must deal with her past indiscretions and her notoriety around Rosewood.

The girls’ lives have been turned upside down by their captivity and each one of them is looking for answers to make sense of their ordeal. Aria focuses on Andrew by trying to figure out who this boy really is while Emily tries to connect with a new friend. In true Spencer fashion, she is on a mission to get answers about Charles from Ali and Jason. Hanna wants to bring the four friends back together so they can move past what happened in the Dollhouse. Meanwhile, Alison is no longer the queen bee/mean girl she once was – but who is she now? A new friend tries to help her find the courage to start anew and find the “new” Alison.

After lying to Alison and Jason about Charles, Kenneth comes clean about the family’s connection to the young boy. While he won’t give much detail about Charles’ past, he say’s enough to give the PLLs a clue of where to look for the missing pieces – Radley Sanitarium. With Radley now closed and the files shipped off to be shredded, the girls must act fast before all traces of Charles’ past disappear. Meanwhile, Caleb’s protective nature starts to pinch Hanna, and Spencer seeks a remedy for her sleeping issues.

With the stalker threatening to kill all of them if they don’t divulge Charlotte’s killer by the election, the PLLs and company, at wit’s end, must boldly fight back. As Spencer and Toby work together to catch Sara Harvey, Yvonne wonders where Toby’s true affections lie. Ezra finishes the last chapter of his book, finally ready to say goodbye to Nicole; Aria comforts him during this emotional time and old feelings bubble to the surface. While Caleb works intently on his plan to protect Hanna, they reflect on what could have been. Meanwhile, Alison experiences strange visions and starts to question her sanity; Emily keeps tabs on her to make sure she’s okay.

Mona returns to Rosewood in a very fragile state as she must answer to the police for faking her death. Matters only get worse when she is confronted by Lesli’s sister about Lesli’s inadvertent involvement in Mona’s plot. Hanna is determined to help Mona out, not only to reassure her she is safe from Alison but also to try and repair Mona’s friendship with Lesli. Emily tries to help Sara with her troubled home life by encouraging her to explore the possibility of emancipation. Spencer, on the other hand, finds help from someone from her past. Meanwhile, Alison grows closer to Lorenzo as she looks for support outside of her family.

After years of tormenting and numerous shocking revelations, Torn between their old habits and their new lives, the events in Rosewood compel the Liars to join forces once again, as relationships are put to the test and secrets are revealed. Having matured over the past few years, these are not the same girls who left Rosewood. As new lies emerge – how will they push forward without going back?

With all signs pointing to Lesli as the tormentor in the hoodie, the PLLs are on a mission to get concrete proof before bringing their findings to the police. But as the girls ramp up their investigation, "A’s" threats escalate. Meanwhile, a friend of Emily’s makes her a surprising offer, and Spencer is pressured by her family to make an important decision.

After Alison is confronted with a sudden, mysterious jeopardy, the Liars decide to take things into their own hands for a counterattack. Hanna and Caleb work together to develop a plan to come face-to-face with the tormentor. Emily and Spencer team up to investigate if Mona had any involvement with the murder. Aria and Ezra continue to work on the book though it might be more difficult than anticipated. Meanwhile, Ali encounters an unexpected visitor.

After the stalker nearly killed Emily, the Liars begin to take the threats more seriously and attempt to keep their mouths shut to prevent any further harm. Caleb must deal with the collateral damage of taking the blame for the leak about Yvonne; Spencer tries to comfort him and get him to tell the truth. Emily goes on a mission to track down who came after her. Aria and Ezra move forward with the novel. Meanwhile, Hanna avoids dealing with her personal life.

As the girls are forced to stay in Rosewood, questions about the new mystery surface. A restless Aria starts to look suspicious as she heads back to Boston a little too quickly. But could Aria really be the one behind this? As Spencer, Emily and Hanna find themselves back in familiar territory, they aren't happy with going about solving this puzzle "the old way." Meanwhile, Emily continues to lie about her life in California and Alison keeps a close eye on her friends.

Aria, Emily, Hanna and Spencer find themselves back in familiar territory with the Rosewood P.D. knocking at their doors looking for answers and their actions now affecting the loved ones around them. With her mother's job on the line, Hanna tries to come up with an alibi that could save all four of them with the help of her old high school friend, Lucas. Meanwhile, Emily comes clean about the last five years, and Aria goes the extra mile to keep Ezra's second book in play with her boss.

In order to prove Sara Harvey is behind the threats, Team Sparia reunites to find evidence of Sara's involvement before they go to the cops. Caleb puts together a plan with Hanna to fight back against the new stalker by using the security footage tapes. Meanwhile, Aria gets unexpected news from her family, and Ali comforts Emily in her time of need.

With the Rosewood P.D. breathing down Hanna's neck about The Radley security footage, she opts to confess the truth to those closest to her in hopes they can help. Aria continues to search for answers, with help from Emily, on whether Ezra is as guilty as he seems. Spencer works together with Caleb to track down the new threat. Meanwhile, there is awkwardness all around when new love interests emerge and old ones resurface.

While new discoveries are made in the investigation of Charlotte's murder, the truth begins to emerge about the Liars' personal lives. Spencer is concerned to learn her mother is keeping a secret of her own. Aria confesses to Liam how deeply she's involved with Ezra's book. Ali admits that she and Elliott are more than just friends. Mona reveals where her true allegiances lie. Caleb, Spencer and Hanna deal with the complications of new relationships. Meanwhile, Emily and Hanna each receive shocking threats that elevate the seriousness of the situation.

As romantic relationships move forward, the Liars investigate a new suspect in the murder case. With Ezra back in Rosewood, Aria must tell him the truth about her involvement with his book. Spencer and Caleb deal with a media leak that affects the campaign. Hanna takes a look at her life after an incident at work. Emily gets harassed by the stalker while she continues the search for Sara. Meanwhile, two lovers finally tie the knot with the help of a special officiant.

Who killed Toby's mother? Who hit Alison in the head with the rock the night she went missing? Who is Red Coat? Who killed Bethany? Who is the Black Widow? Why has "A" been targeting the PLLs all this time? After years of torture, Alison, Aria, Emily, Hanna and Spencer finally come face-to-face with their tormentor and learn the story of how and why Charles became "A."