Jennifer Simpson is a child from the fictional Granite Orphanage in Romsdalen, Norway. She and her friends, who are also orphans (Laura, Ann and Lotte) are adopted in September 1995 (the same month the game was released) by a wealthy recluse named Mr. Barrows, who lives in a mansion known as the "Clock Tower", named after its most predominant feature.

The game immediately begins with these characters walking towards the Barrows mansion and settling in the main foyer. Mary, the woman who brought the children to the mansion, leaves to find Mr. Barrows, but she takes an unusually long time. Jennifer offers to investigate, but upon leaving the room, a scream is heard from the main foyer. Jennifer returns to find the lights are off and the girls are missing. She soon finds herself being stalked after finding either Laura or Ann killed by a murderous little boy with deformed features, wielding a huge pair of scissors. The boy is Bobby Barrows, the Scissorman, who will be Jennifer's main stalker and tormentor for the rest of the game.

While exploring the mansion, Jennifer will need to find out Mary's true intentions - either by discovering Simon Barrows trapped in a jail cell inside the courtyard, or by discovering her father's corpse in a hidden room. If the former happens, Jennifer will need to give him a piece of ham as food. If the latter happens, Jennifer will find his death letter that tells of his account about Mary Barrows and her twins, Bobby and Dan. It says that he was trapped there for three days, until his death on November 10, 1986.

Jennifer visits a small, occult-looking church. However, to obtain the key to that church, Jennifer fights off a possessed doll in Bobby's room that tries to kill her. If the player has collected all the necessary items and clues, then Jennifer is able to gain access to the underground catacombs of the mansion - using either the Devil Idol or the Sceptor, but the former is canonical as it appears in the sequel. Jennifer sees a cloaked figure walking ahead of her; this is Mary. She follows it, wearing a disguise to fool the guard dog using Mary's perfume, and a black cloak found in the mansion. If she did not need to rescue Jennifer from the jail cell, Lotte can be found dying at an altar, and tells Jennifer about the switches in the clock tower. Otherwise, she rescues Jennifer from the jail cell, but is shot by a threatening Mary.

Jennifer enters a room, where she discovers the humongous Dan Barrows, hidden within curtains. At that point, the awakened Dan chases down Jennifer to a steep cliff. She successfully climbs over, knocking down a can of kerosene which splashes onto a nearby candle. This triggers an explosion that immolates Dan, and Jennifer rides an elevator in the catacombs. She ends up defeating Bobby in the clock tower, and Mary as well in (or around, depending on prior actions) the clock tower. If Ann (or Laura) had not died yet, then this survivor would reunite with Jennifer at the clock tower, but later be thrown down the tower by Mary. These actions would lead to one of Endings A, B, or C - any of these could be canonical according to the events of the next game. Because of the game's open-ended nature, the player can also discover a number of other endings.

Characters

• Jennifer Simpson

Jennifer is the primary protagonist and was made an orphan when Walter was killed by Mary Barrows to cover-up the birth of her demon sons. She wears a dark blue dress and a white blouse.

• Dr. Walter Simpson

Walter is Jennifer's father. His corpse can be found in a hidden room, with the door covered with plaster. Jennifer can uncover and destroy this wall. A few medical charts show his patients' (Mary, Dan and Bobby) names. He is identified by Jennifer when she discovers his medical bag on the floor, with his name printed on it. Jennifer can examine the body, and find a memo which triggers a cutscene showing her holding his dead body, while reading the note. The note explains that he had been called to help Mary deliver the boys. After they were born, Dan and Bobby devoured his right hand. He knew something was very wrong with the boys, which caused Mary to hide him in a room, and plaster the door shut.

• Ann (Anne)

Ann is Jennifer's brunette friend. She is the oldest of the four girls and she teases Lotte about being "paranoid". She has long brown hair and wears a long green dress with her top as a yellow blouse topped off with a brown vest. Ann dies in different ways. She can be thrown out a window, drowned in the pool or impaled through a stained glass skylight by Bobby. She (like Laura) can be thrown off the clock tower by Mary. If she survives, she will appear in endings A and S.

• Lotte

Lotte is Jennifer's best friend. She has short red hair and wears a plaid shirt with blue jeans. She is uneasy about the Barrows Mansion. Lotte rescues Jennifer from Simon Barrows' cage before being shot by Mary. If the player does not see this, Lotte will be found in the caves. Unlike Ann and Laura, Lotte can't be saved.

• Laura Harrington (Rolla Harrington)

Laura is Jennifer's blond friend, wearing a blue dress. Laura can be found either hanging from a shower or inside a suit of armor. She (like Ann) can be thrown off the clock tower by Mary. If she survives, she will appear in endings A and S. Her surname is revealed in the novel.

• Mary Barrows (Mary Burroughs)

Mary is Simon Barrows' wife and the primary antagonist of the game, although she is seemingly kind when she takes the girls to the Clock Tower mansion. Mary is a curvaceous woman with blond hair. She is the mother of Bobby and Dan, the demonic twins. She is involved in occult activities. She is killed either from falling off the tower while being plucked by crows that Jennifer saved, being thrown by Jennifer into the electric generator box after Mary tried to choke her to death, or lose her grip on a ladder leading to the clock tower while trying to push Jennifer off of it.

• Bobby Barrows (Bobby Burroughs)

Bobby is the 'Scissorman' and the secondary antagonist of the game. Bobby is a short 9-year-old dressed in a school uniform who wields a pair of scissors. Bobby can be found by entering certain rooms, examining certain items and sometimes remaining in an area for a period of time. Bobby never talks, although he makes swift, high-pitched giggles whenever Jennifer is in terror (while dancing in enjoyment) or is about to sneak up on her, and his face is deformed. He dies after falling off the clock tower, due to the bells' chimes disorienting him.

• Dan Barrows (Dan Burroughs)

Dan is the deformed brother of Bobby and the minor antagonist of the game. Dan is a purple, fleshy beast that spends his time in the caves. When Jennifer finds him, he gives chase but is "killed" when she accidentally ignites a can of explosive kerosene on a candle. Dan reappears in Clock Tower as a amnesiac schoolboy (and also survived the events in this game) named Edward, and takes up the role of the Scissorman. How Dan survived is never revealed, but the PlayStation version has a cut scene showing Edward rising from the charred remains of Dan.

• Simon Barrows (Simon Burroughs)

Simon is the supposed adopter. He is Mary's husband and the father of her twins. For some reason, Mary locks him in a cage. Due to being imprisoned for a long period and the lack of food, Simon becomes insane. As one of Jennifer's deaths, he can try to eat her if she does not give him the ham from the kitchen.

Endings

Clock Tower has a variety of endings depending on the choices the player makes throughout the game. The endings run from A to H, H being the worst and A being the best, with a special S ending above A. Endings A, B, and C seem to be canonical, as the sequel Clock Tower (Clock Tower 2) is compatible with any of these endings.

• Ending S

This ending is non-canonical and the most difficult to obtain. In the initial list of endings, if it has not been unlocked, it is not shown at all. Jennifer's friend is seen lying unconscious on the floor. Bobby falls to his death after Jennifer activates the clock tower, with the sound of the bells disorienting him. Mary attacks Jennifer but is pushed back and then off the tower by an enraged flock of crows, one of which Jennifer freed from a cage earlier in the game. Jennifer is then joined by her one surviving friend for the credits. (If Jennifer saw Ann die, then Laura will join her, and vice versa. Lotte can't be saved.) Two of the requirements are freeing the crows, and discovering Walter's secret room.

• Ending A

If Jennifer encounters Simon Barrows in the shed, and one of her friends survives, this ending is unlocked. After Bobby falls to his death, the surviving friend runs to Jennifer. Their reunion is cut short when Mary steps out from the shadows and tries to grab Jennifer but instead throws Jennifer's friend into the Clock Tower's gears. Mary is defeated when Jennifer/the crows pulls her off of the side as Mary attempts to stab her. Jennifer is the only survivor.

• Ending B

Having seen all her friends die (and/or failing to free the crows), Jennifer goes to the third floor using the elevator. Just before the elevator stops, Bobby attempts to break into it using an overhead vent. Jennifer escapes to the top of the clock tower using a ladder, and activates the clock tower bells with the switches, disorienting Bobby enough so that he falls off the top of the tower to his presumed death. Mary, hysterical at the deaths of her two children, attempts to throttle Jennifer. Jennifer throws Mary into a generator box, electrocuting her. Jennifer is the only survivor.

• Ending C

Inside the elevator, Jennifer presses the button for the second floor, and finds Mary in the hall. Having seen her father's corpse or having been confronted by Mary in the shed, Jennifer talks to Mary before she attacks her with a knife. Mary then calls for Bobby to help her. Jennifer avoids Mary and climbs up a ladder to reach the clock tower. However, Mary grabs Jennifer's leg while she is climbing. Jennifer breaks free of Mary's grip and she is flung off the ladder to her death. At the top of the clock tower, Jennifer faces Bobby again who is out to avenge his mother and brother, but she activates the clock's bells. The bell's chimes disorient Bobby enough so that he falls off the top of the tower to his death. Jennifer is the only survivor.

• Ending D

Inside the elevator, Jennifer presses the button for the second floor, and finds Mary in the hall. Having not seen her father's corpse, Jennifer talks to Mary and Mary consoles her, telling her that "You're safe now". Jennifer runs towards Mary at which point Mary stabs Jennifer in the chest with a knife. With her dying breath, Jennifer asks "Why" and Mary stands there with an evil grin. There is an alternate Ending D, see below.

• Ending E

Inside the elevator, Jennifer presses the button for the third floor, and the elevator suddenly halts. Bobby breaks into the elevator through an overhead vent, Jennifer screams and the screen fades to black.

• Ending F

If Jennifer does not see Lotte die, she will continue the game normally until the elevator sequence. Upon entering the elevator, the doors close. Bobby attacks Jennifer off-screen, and blood seeps from under the elevator doors.

• Ending G

If Jennifer sees two of her friends die, she will leave in the car, escaping the mansion and return to the orphanage. A text cut scene tells that Jennifer was found dead three days later in her room. The cause of this ending is unclear; the most common theories that she is killed by one or more of the Barrows, or that Jennifer committed suicide over the loss of her friends.

• Ending H

This ending is considered the "worst". Jennifer stumbles across a car in the garage, and finds the key in a crate. She is unable to leave her friends in the mansion, but after three attempts to enter the car, she eventually gives in and escapes, driving through the wall of the shed. In the ensuing cut scene, a pair of scissors can be seen from the back seat, Jennifer appears shocked, and screams. The screen then fades to black.

• Alternate Endings

There are two endings that can be obtained through a glitch in the game in which Jennifer does not see Ann or Laura die. The first is identical to endings H and G, but only displays the credits after Jennifer leaves; this results in a Ranking of D. The second is obtained if the player meets the prerequisites for Ending S, but it is identical to Ending F.

It has been stated by the producers of the game that the game design was inspired by Dario Argento's Phenomena (known as Creepers in the US). This is likely because the film and the game share similarities, including the name and basic appearance of the leading character (Jennifer), a deformed killer child and a deranged mother. There are some additional comparisons to Argento's other supernatural thrillers that may be seen in Clock Tower's presentation. Also in Suspiria, the opening death scene is of a woman falling though a red rosette-window in a manner which is almost identical to one of the opening death scenes found in the game. Some of the character traits and actions, particularly those of Mary Barrows, also share similarities with those in Argento's 1975 movie "Profondo Rosso".