Three years younger than her sister, Harper admired Charlotte very much and the two girls were very close. When their cousin Clara's mother died, Clara came to live with them and was treated like a sister. Eleven years later, Harper's own parents died together in a plane crash, making Charlotte the new head of the Thornton family business. Even so, the girls managed to stick together until Charlotte's death in 1989.
Harper was absolutely devastated by her big sister's death. Clara describes her as being "torn to shreds by the whole thing". Wade says that Harper "got lost in that night and never got found". At the funeral, Harper had a "violent outburst" causing thousands of dollars of damage and a few minor injuries, leading her to be carried out of the service by police. No charges were pressed and she was released into the care of her family. A police spokesperson noted that Harper had seemed to think the justice hadn't been served in the case of her sister. Harper in fact blamed Clara for her sister's death and was convinced that Clara stole the necklace Charlotte was wearing the night she died. When Harper confronted Clara about it, becoming so upset she pushed her off the widow's walk. By the time Clara came out of the hospital, Harper was nowhere to be found. She was gone for so long the family began to think that she had died too, causing her grandfather to have a gravestone made bearing her name. But one day Harper came back "as wild and thin as a spring sapling" according to Wade. Her grandfather was so furious that she made them worry all that time that he left her gravestone in the cemetery as a reminder of what she put them through. She would sit on it and read.
At one point Harper claims she became the first Thornton to be sent to the Millicent P. Krauthammer Sanitarium for Criminally Insane Girls and Women of Good Social Standing and was one of the few to actually graduate from the place. She was told that she was going to the most elite boarding school on the east coast, and she believed them until they drove up and she saw the bars on the windows.
When Jessalyn Thornton goes missing in 2013, Nancy is asked by Savannah Woodham to go in her place to Thornton Hall to find her. Eventually, Nancy finds a note addressed to her on a small table near her sleeping bag, instructing her to put on a blindfold and recite Charlotte's rhyme to meet her ghost. After Nancy recites the rhyme correctly, she is forcibly led down to the basement. When Nancy is finally able to take off her blindfold, she meets her "ghostly" kidnapper, Harper, who is hiding from her family. She dramatically explains that she is "a grandly unbalanced sociopath with delusions of granduer, a history of erratic behavior and violent tendencies". Harper continues to leave "ghost notes" for Nancy, singing eerily each time to signal she's written a new one. She also tells Nancy to talk to Clara about subjects that bother her. When Nancy asks why, she says that she wants Clara to be sad. At one point Nancy mentions that the fireplace Harper is using may not be safe to use, but Harper dismisses Nancy's concerns, saying that it sounds like an "upstairs people" problem.
Nancy eventually finds Jessalyn hiding in a tunnel in the basement. She explains to Nancy that during her bachelorette party, Harper found her and told her about how she thinks Clara killed Charlotte and stole her necklace. All her life, Clara told her that Harper was insane, but Jessalyn listened to what Harper had to say because her mother always seemed so cold to her, and what Harper said made sense of her mother's behavior. All this time, Jessalyn and Harper have been working together, even dressing up as Charlotte, in order to scare Clara away from the briefcase where she keeps Charlotte's necklace. The necklace, an heirloom from their civil-war-spy ancestor, contains a clue to opening a safe. Nancy manages to swipe the necklace and open its locket, revealing not only the safe clue but also a message saying that Clara can't be trusted. Jessalyn goes to confront her mother herself while Nancy opens the safe, which turns out to contain Charlotte's will. Though originally it stated that everything was to be Clara's in the event of Charlotte's death, she had revised it the day before she died, making Harper the one to receive everything instead of Clara.
After Nancy reads the will, she notices that Thornton Hall has caught on fire.
Nancy can choose to help Jessalyn rescue Harper, but if Nancy refuses to, both Jessalyn and Harper are hospitalized and the Thorntons angrily refuse to speak to Nancy. If Nancy helps build a wheelbarrow to evacuate Harper and then goes to save Clara, Harper disappears shortly after the fire. After an exhaustive search, Wade and Jessalyn track her down and convince her to rejoin the family. Harper agrees, but has Thornton Hall completely razed, replacing it with a public park dedicated to all the lives lost on Blackrock Island.
- Harper sings eerily to let Nancy know she has left her a "ghost note", appearing to be just as lovely a singer as her sister Charlotte.
- Sometimes Harper fondly calls Jessalyn by the nickname "lamb".
- "I don't function well in reality."
- "Shh. Use your inside-of-a-crypt voice."
- "The neighborhood children used to call me “witch lady” until my dedication to the ironic led me to bake cookies for the sweet darlings. But it was my love of the dramatic reversal that won out in the end, and I threw the little runts down a well!"
- "Am I dressing up as my dead sister for kicks after the only family member everyone can agree on has gone missing? Is that what you're asking?"
- "Golden child, Charlotte. She was perfect in everyone's eyes, even mine. I wanted to be her when I grew up. But then one day I was older than my older sister, and older still today."
- "She's a big girl now. The truth shouldn't upset her. Don't look at me like that! I'm bored down here and she's done worse to me."
- "I got a little diploma that says 'Harper's no longer a danger to herself or others' and everything."