Vastly improving on the the Gummi Ship System on that first Kingdom Hearts, the Gummi Ship system has downgraded as the main traveling system from world to world to essentially the minigame of Kingdom Hearts II. Unlike in the first Kingdom Hearts, the Gummi ships are far more customizable, such as the ability to add on side-ally ships that can help you when you are shooting down the enemy ships. Not only that, the enemy ships are alot faster, and the attacks you can deal are alot faster than before. The Heartless and Nobody ships are also better and come faster than before, and the fast-paced Gummi Ship battles make it much more of an appeal than the first Kingdom Hearts' Gummi Ship battles. Similar to the main game, you'll be able to perform Reaction Commands, An improved score system, and the ability to pick up mid-flight bonuses, you can turn your whole ship around, during flight's you can fight bosses, there are multiple routes you can take while flying. Differently, the buttons you use such as the ability to fire more than one shot at a time, so the effectiveness of your assult on the Gummi Ship minigame. In Kingdom Hearts 2 scoring is judged by a similar system. When you destroy an enemy your score will go up. Different enemies have different point values.

Although the mechanics of the Gummi Ship have improved, and it has a feel of a space shooter, its still not as fun as most expect it to be, at times it may seem highly trivial, and usless. The turnaround and radar system were also added, it provides a different view of shooting and destroying enemy ships, but it can feel a bit strange, and the attacks on you become so much more relentless. It varies as well, the changes made become very 'intense' to a moment, as the enemy ships pile, but it still doesn't change the feel, the controls are still awakard and they are even worse because of the constant use of the 'x' button, and the switch between camera views makes it alot more harder to control. The stages and levels on where you fight, become alot more diffcult to maneuver with the limited space in mind, and with the enemy entourage attacking, the controls become even harder to control. With that in mind, Although the Gummi Ship 'Minigame' is diffcult and hard with the controls, it still is somewhat enjoyable.