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 wildly. Terrified, Alyssa dashes from the room-and is transported back in time, to London, circa World War II. While there, she begins to explore the city, which is constantly bombarded. Her search leads her to a tailor shop-where she witnesses the gruesome murder of a young girl at a piano. 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; 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 mad man with a sledgehammer. By restoring a precious pocket watch belonging to the young girl's father, the girl's spirit is eased. This breaks the power of the mysterious Sledgehammer, who engages Alyssa in battle. Her vial of Holy Water becomes a crossbow, and she destroys the villain in a shower of golden light. May's spirit reunites with her father's ghost, and the two thank Alyssa before ascending into Heaven. Alyssa also claims a small portion of a pendant.
When Alyssa returns to the present day, she begins to delve into what happened, and learns a surprising secret about 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"- that 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; 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 new knowledge, she moves back in time again and confronts the Corroder, a frightening man who murdered an elderly woman and her son by throwing them in a vat of sulfuric acid. Files reveal that the Corroder was related to the two, the younger man being his cousin. Alyssa finds an old shawl that proves to be the key to freeing the mother and her son, and destroys the Corroder.
Upon returning home, though, Alyssa begins to wonder as to why her mother wanted her to stay away. Soon, she realizes that the mysterious "Dark Gentleman" hopes to gain immortality by becoming an Entity using the the Ritual of Engagement. That dark ritual requires the "heart of a Rooder" of the same bloodline. Alyssa's heart! Alyssa meets other Rooders who were subjected to this torment as she fights the evil Chopper, the leader of the earthly Subordinates. The spirits of the young women help her overcome the villain, and she is able to vanquish the villainous Chopper.
After completing this mission, Alyssa is warped back in time once more-to the home of the mysterious Lord Burroughs, who lived on the very land that the boarding house stands on in the present day. Now, though, it is the location of the titular clock tower. Burroughs, obsessed with the secrets of the Entities and Subordinates, hires two to murder people for him-the Oriental twins, Scissorman and Scissorwoman. Burroughs plotted to become an Entity himself; however, his daughter died on the eve of her fifteenth birthday, ruining his plan and driving him insane. He dies, and Alyssa overcomes the Scissor twins.
Once Alyssa returns to the present day, she discovers that the villain behind her mother's disappearance is...her own grandfather, Richard Hamilton! Richard 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, then The tower collapses, and the evil spell of the Subordinates Alyssa destroyed is finally lifted forever. 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 then runs over to hug Dennis nearby.
Innocents slain by the Subordinates haunt each stage and will attack Alyssa if she approaches them, sending her into panic. In order to pacify these spirits, an item of sentimental value must be found and returned to the spirit's corpse, which always lays near the area being haunted.
After each scenario, Alyssa must confront the subordinate who has been stalking her. At this point her holy water bottle transforms into a longbow, allowing her to fight back. Each battle is confined to a single area, and the player must defeat the subordinate in order to progress. The health of both Alyssa and the subordinate is measured by two life bars which appear on-screen. Alyssa must dodge or duck attacks whilst firing arrows at her attacker. In order to inflict considerable damage, shots must be powered-up. These shots tether the subordinate to the ground. Whilst powering-up the shot, Alyssa must stand still and cannot adjust her aim, leaving her vulnerable to attacks and making it possible for her enemy to move out of her line of sight. If the boss is transfixed with multiple powered-up shots, Alyssa performs a highly damaging attack with her next shot, killing or severely wounding the subordinate.
The game's protagonist. Without knowing why, she was sent to a boarding school by her mother and told not to return for six years.
Alyssa's mother. The two are very close, but Nancy appears to be hiding something from Alyssa.
A boy that Alyssa knew in primary school three years prior to the game's events. Dennis appears unexpectedly at Alyssa's home near the start of the game. He appears to have a crush on Alyssa, and is obsessed with staying as close to her as possible. He is the one who kills Scissor man by impaling him with a pendulum.
Alyssa's grandfather, who took the task of raising Alyssa after her father died. He seems to dislike Nancy's choice of husband, and is cold hearted toward him. Three years before events of the game, Dick disappeared from the Hamilton Household and has not been seen since. His disappearance depresses Alyssa, and she waits anxiously for his return. He, is the main antagonist, along with his and Alyssa's ancestor, Lord Burroughs.
May is a child dedicated to playing the piano. She entered a piano competition, hoping to win so that her music would be broadcast over the radio, and heard by her father, a soldier at war. May was bludgeoned to death by Sledgehammer after the competition, and it was revealed that her father died in battle.
The father of May Norton, and a soldier at war. He cares a lot about his daughter, and is disappointed that he has to leave her alone at the tailor shop. Before Sledgehammer killed May, William was killed out at the battlefield, and May never knew he died because of her murder.
Dorothy is a blind old woman, who is the mother of Albert. She is very caring, and is sick of people fussing over her health, and tries to give out the feeling that she is happy without sight, but she really isn't. She would give anything to be able to see again, and wonders what her son does all day in his shed making toys.
Albert was also a victim of Corroder, and the son of Dorothy. He is very protective of his mother, and looks after her as much as he can. Dorothy believes he is too over protective of her. He is a man who gives and expects nothing in return by making children's toys for a living.
Alyssa's real father. Alyssa knows nothing about him as he died shortly after she was born. But later, it is revealed that her dad was murdered by her grandfather when he threw Philip over a balcony, causing his head to fall onto an axe, splitting his head. If Alyssa opens a sealed door in the house, she will open a bathroom with a rotting corpse in the bathtub along with an angry spirit. Whether or not this is her father is unknown.
Linda is a missionary nurse, currently positioned in Africa. She is also Dennis's big sister, who has raised Dennis ever since his birth. She has told Dennis she will not be back for at least six months, but mysteriously appears again during Alyssa's journey.
This enigmatic character is dressed in dark clothes and has an unusually deep voice. He seems to know a lot about Alyssa, and carries a strong love for her. Alyssa does not know who he is, but thinks that it is obviously one of her mother's lodgers. But there might be more to him that meets the eye: He is Dick Hamilton.
Sledgehammer is the first boss encountered in the game, found bludgeoning a twelve-year-old pianist to death on Christmas Eve 1942. Prior to becoming Sledgehammer, he was known as Robert Morris, a stonecutter.
Corroder is the second boss encountered in the game; he is seen blinding an elderly woman and her adult son before throwing them both alive in a drum of acid in 1963. Corroder's real name, John Haigh, as well as his modus operandi of killing his victims, is inspired by the real John Haigh, who was known in Britain as the Acid Bath Murderer. He was related to Dorothy and Albert.
Chopper is the third boss and head of the Subordinates. Born in 1655 as Harold Powell, he was a woodcutter who was seriously deformed at birth and as a result, was taunted and cursed for his appearance. When Powell was 17, he proposed marriage to Emily Dickins, the innkeeper's daughter, but was cruelly rejected. In turn, he dismembered Emily with his axe and continued to murder other women in the same fashion for 2 more years until he was later on caught and trialed.
Known as Jemima and Ralph respectively, they were sadistic, sought pleasure in torturing people to death and had a fascination with blades, scissors in particular. Their origins before being brought to Lord Burroughs's estate are unknown, though it is said in a file during the game that it is believed the twins came from the Orient. Both twins, Jemima and Ralph actually share the same Entity.
British lord who had a sadistic side and enjoyed watching people die. He hired the Scissor twins (see above) to do most of his dirty work. He was a strong believer in the Entities and tried to gain power by using his daughter in the Ritual of Engagement, but she died in an accident just before her 15th birthday. Her death sent Lord Burroughs into a deep rage, resulting in him killing many. However, he was eventually overcome by his people who forced him over the clock tower of his castle, where he fell into the gears. He's not exactly a Subordinate as he came back to life by Dick, not by an Entity. He's the final boss of the game.
The only weapon Alyssa is armed with. The holy water is of limited use and can remove blue crests on doors, stun enemies and activate holy portals. The only way to refill your holy water vial is to find a lion's fountain, or a jar of it. This is the most useful piece of equipment Alyssa will get her hands on with the exception of the crossbow. When pressing the triangle button, Alyssa will throw a dose in an arch ahead of her. It will stun enemies reaching contact with the splash.
Once the sentimental item belonging to the greater spirits whose misery is powering the level's killer is found, Alyssa gains the power to face off against the killer in battle, using a divine bow and arrow. Pressing triangle will make Alyssa to shoot an arrow. The longer you hold the button, the more powerful effect the arrow will have. The thing about these boss battles, however, is that you must not keep on pounding them with arrows until they fall dead, it will take a very long time. You need to hit them with fully charged arrows, which pin them to the ground with golden chains of light. You cannot shoot three arrows standing still however, you must shoot it so it binds the enemy, tying them down from three different angles. After three chains are placed, Alyssa will launch an arrow high into the air, which will then turn into a massive Rooder attack. This does a lot of damage, and may kill the enemy. Some of these attacks may not defeat powerful enemies, and may need to be performed more than once. A boss's life bar depends on how many people they killed. Right before the fight, a message that says "sentenced to" appears, along with a number. The number gets lower as the boss's health bar fills up.
Green repellant arrows do damage and knock your enemy back, giving Alyssa some time to run back a bit and charge a golden arrow up. These are very helpful in boss battle, so use them with care.
These arrows are equivalent to the charged up golden arrows, and have the same effect. They bind the enemy with one golden chain.
Returns the player's Panic Meter to zero over a period of time.
Protects Alyssa from a single blow. They are used automatically when an attack would hurt or kill Alyssa, such as when in full panic mode. They are unavailable in boss battles, and do not prevent death by scripted events.
Makes Alyssa invisible for a short period of time.
Pacifies a murder victim's spirit, preventing it from harming Alyssa.