Following its predecessors, Clock Tower II is a point-and-click adventure game with 3D graphics. The player can use either a standard PlayStation controller or mouse to control the protagonist, Alyssa Hale, through the game. The cursor will change shape when placed over certain objects, which the player can click to interact with. Clicking in any location will guide the Alyssa in that direction. Moving the cursor to the top of the screen will reveal the player's inventory. Clicking an item and then clicking an object on the screen will use the item on that object or in that location. Alyssa starts the game with an amulet which keeps her alter ego, Mr. Bates, from emerging and controlling her. However, the amulet can be placed within cases or other containers. Without the amulet, Alyssa will become Mr. Bates if provoked with fear. To change back to Alyssa, the player needs to simply retrieve the amulet back. Some events can only be cleared as Mr. Bates and likewise some only as Alyssa. The choices the player makes as both Alyssa and Mr. Bates will change the scenario development and lead to one of 13 possible endings. When Alyssa is being chased or is in danger, the cursor will flash red. During this panic mode, the player must rapidly tap a button to escape. When escaping enemies, click points will appear on items or objects that Alyssa can use to fight back or hide from the enemy. Escape mode will not end until the enemy is repulsed or successfully evaded. If playing as Mr. Bates, the player may use obtained weapons against the enemies. When equipped with a weapon, the cursor becomes a crosshair used to aim and shoot. The cursor will change color during panic mode from white, to yellow, and finally red to indicate the Alyssa's stamina. First aid kits can be used to reduce stamina by one level. If Alyssa's stamina reaches zero or the player fails a panic scenario, the screen will read "game over" and provide the player the option to restart from the last room they entered with one extra stamina level.