Alyssa Hamilton, a 14-year old girl living at a boarding school, receives a strange letter from her mother, Nancy, telling her she must hide until her fifteenth birthday passes. Alyssa is naturally worried, and so decides to go against her mother's wishes and return to her childhood home, a boarding house. When she arrives, her mother is missing, and the only other living person in the house is a mysterious stranger, known as the Dark Gentleman. He offers Alyssa cryptic warnings and clues as to her mother's fate.
Though frightened, Alyssa becomes determined to find her mother. She explores the house and finds a vial of holy water, along with strange symbols on doors that only the sacred water can break. Eventually, her search leads her into her mother's room, where a piano begins to play Frédéric Chopin's Fantaisie-Impromptu wildly. Terrified, Alyssa dashes from the room and istransported back in time, to London, during World War II. While there, she begins to explore the city, which is being constantly bombarded. Her search leads her to a tailor shop, where she witnesses the gruesome murder of a young girl. The crime is perpetrated by a mysterious man wielding a sledgehammer; he notices Alyssa, and begins an obsessed search for her. As Alyssa evades him, she runs into other angry ghosts, but by returning particular items to each spirit, she is able to placate them and lay them to rest. Eventually, Alyssa pieces together the mystery: May Norton, a 12-year-old piano-playing prodigy, was brutally murdered on Christmas Eve by a madman with a sledgehammer. While still exploring the tailor shop, Alyssa sees memories from the past; when May's father tells her that he is going to war, she gives him a Pocket watch as a reminder of his wife and May. While in battle, he is hit by an explosion and lands on a row of barb wire, dying instantly. Alyssa decides to free May's spirit, which is trapped on earth, but on her way to do this, she is confronted by the killer. Her vial of Holy Water becomes a longbow, and she destroys the villain in a shower of golden light. Alyssa gives the pocket watch to May's spirit, who proceeds to play the piano once more. After a short while, May is reunited with her father, and the two thank Alyssa before ascending into Heaven. At that moment, Alyssa faints.
She wakes up in her room, lying on the bed, believing it was a dream. Her childhood friend, Dennis knocks on the window while hanging on to the windowsill. Alyssa helps him up, in anger, wondering why he would try to enter her residence, and Dennis gives the key to her grandfather's room to Alyssa. While searching through the room, she learns about a surprising secret in her family. The girls in her lineage are known as "Rooders", young women with the supernatural ability to communicate with the dead. She also learns of a ferocious dark power-called an "Entity", which can infect certain humans and drive them to acts of crazed murder. The agony and despair of the souls of the murderer's victims feeds their dark power, and grants the villain - now known as a "Subordinate" - immortality. The Rooders are fated to find and free those tortured souls, breaking the Subordinate's magic and allowing them to be destroyed. These powers peak at the age of fifteen, and wane afterward, disappearing completely at age 20; therefore, the women in Alyssa's family marry young and quickly bear a daughter.
Alyssa realizes that she is a Rooder, and that Sledgehammer was a Subordinate, feeding off of young May's soul. With this new knowledge, she moves back in time again. She enters a house with a blind elderly woman and her son. Alyssa then looks at a memory where the man and his mother are murdered viciously. During the struggle, the shawl that the son made for his mother drops into a sewer. Files reveal that the murderer, known as The Corroder, was related to the two, the younger man being his cousin. Alyssa finds the old shawl, and destroys Corroder, freeing the mother and her son.
Upon returning home, Alyssa begins to wonder why her mother wanted her to stay away. Soon, she realizes that the mysterious "Dark Gentleman" hopes to gain immortality by becoming an Entity himself, using the Ritual of Engagement. This dark ritual requires the "heart of a Rooder". When the Clock tower begins to form, Alyssa is sent to the top of the tower to confront the Dark Gentlemen. He throws her down the tower, sending her to the valve room. Regaining consciousness, she confronts another Subordinate, Chopper. After temporarily escaping from him, Alyssa looks back at a memory from when she had just been born. Hearing a scream from the stair balcony, Alyssa runs to find her father struggling with her grandfather. Her father is thrown off the balcony onto an axe head, splitting his head in half. Alyssa denies that her grandfather truly meant to kill her father and engages in a battle with Chopper, but fails to kill him and is sent to a graveyard. Once there, she meets the spirits of other Rooders who lost battles against the Subordinates. Alyssa fights Chopper again and, with the help from the Rooder spirits, is able to vanquish him.
After completing this mission, Alyssa is warped in time once more to the home of the mysterious Lord Burroughs, who lived on the very land that Alyssa's house now resides upon. At this point in time it is the location of the titular clock tower. Burroughs, obsessed with the secrets of the Entities and Subordinates, hires the homicidal twins, Scissorman and Scissorwoman, to murder for him. Burroughs plotted to become an Entity himself; however, his daughter died on the eve of her fifteenth birthday, ruining his plans and driving him insane. He was ultimately crushed in the clock tower's gears, swearing revenge. Meanwhile, with the help of Dennis, Alyssa overcomes the twins.
Once Alyssa returns to the present, she discovers that the villain behind her mother's disappearance is her own grandfather, who lived with the pair since Alyssa was a child, and performed extensive research on the Rooder powers. However, he was descended from Burroughs, and was eventually driven insane by the connections between his and his ancestor's situations, and allowed Burrough's evil spirit to fuse with him. He destroys Alyssa's mother and plots to fulfill Burrough's plan with Alyssa's heart; however, Nancy transfers what is left of her own Rooder power into Alyssa, granting her the strength to destroy her grandfather and Burroughs. After she defeats him, she immediately reunites with her mother. The tower then collapses and the evil spell of the Subordinates is permanently lifted. However, as Entities still exist, the Rooders' fight is far from over. The final scenes shows Alyssa waking up in a field of flowers clutching her clover pendant, as she runs over to hug Dennis nearby. Smiling, she says, "Mom...we did it. We did it, Mom."