Like many traditional role-playing games, Kingdom Hearts II features an experience point system which determines character development. As enemies are defeated, the player gains experience which culminates in a "level up", in which the playable characters grow stronger and gain access to new abilities. As in the first game, Kingdom Hearts II allows a certain degree of character customization through a short tutorial found at the beginning of the game.
Combat in Kingdom Hearts II is in real-time and involves button presses which initiate attacks by the on-screen character. A role-playing game menu, similar to those found in Final Fantasy games, at the bottom left of the screen provides other combat options such as using magic, summoning beings to assist in battle, or executing combination attacks with other party members. A new feature is the "Reaction Command", special enemy-specific attacks that are triggered when the player presses the triangle button at the correct time during battle. Reaction Commands can be used to defeat regular enemies or avoid damage, and are sometimes necessary to complete a boss battle. In addition to the main character, two party members are usually present who also participate in combat. Although these characters are computer-controlled, the player is allowed to customize their behavior to a certain extent through the menu screen, such as attacking the same enemy Sora targets.
In response to criticism, the "Gummi Ship" feature of the first game was re-imagined to be "more enjoyable". Although retaining its basic purpose of travel, the previous system was completely redone to resemble a combination of rail shooter and "Disney theme park ride". In the world map, the player must now control the Gummi Ship from a top-down view and fly to the world the player wishes to enter. Worlds are no longer open from the beginning—the player must unlock the routes to them by entering a new level, controlling the ship from a third-person point of view, and battling enemy ships. After the route is opened, travel to the world is unimpeded—unless it is blocked due to a plot related event.