The player must guide Alyssa through various environments, altering between her normal and twisted personality, to uncover the secrets of her and her family's past.

Journalists heavily criticized the gameplay which they found to be poor due to its slow and dated point-and-click interface, as well as its reliance on trial-and-error mechanics.

Following its predecessors, Clock Tower II is a point-and-click adventure game with 3D graphics and survival horror elements.

The cursor changes color during panic mode from white, to yellow, and finally red to indicate Alyssa's stamina.

[3]: 14 Alyssa Hale is a 17-year-old high school girl who, during the spring of 1999, is on her way to a distant town in California to visit her father's friend Phillip Tate.

She hears a series of odd noises through the home and eventually finds Philip, who requests that she burn a statue related to the Maxwell Curse.

She wakes up in a zombie-infested hospital and meets a detective named Alex Corey, who saved Alyssa from the house and tells her Stephanie will survive her injuries.

She soon finds a man armed with a hatchet and wearing an oni mask named George Maxwell, who begins to stalk her.

[16] The gameplay was found to be flawed due to the dual personality mechanic and poor storytelling methods.

[1] Mark MacDonald writing for Official U.S. PlayStation Magazine shared these sentiments, saying the player spends most of their time wandering around, hoping to trigger the next event.

[1] Marc Nix of IGN argued the sound design was good and the graphics were clear and sharp but the scenery was ultimately lifeless.

[1][14][15] Mark Kanarick of AllGame heavily criticized the voice acting, describing it as the worst aspect of the game.

[2] Ultimately, Fielder could not recommend Clock Tower II as an adventure or horror game, saying "leave this one for the antique collectors".

He described it as a terrible game in a conventional sense, but like a cult film, it is redeemed by its willingness to take risks and stand apart from the mainstream and therefore is "strictly for hardcore niche gamers".

[15] Kanarick called it a poor attempt at a survival horror game, but that fans of Clock Tower (1996) may enjoy it.

[2] The Electric Playground presented Clock Tower II with its 1999 "Console Adventure Game of the Year" award.

The editors called it "decidedly the best of the few challengers" in its field, despite competition from the PlayStation release of Broken Sword II: The Smoking Mirror.