The primary goal in each route is simply to make it through the course alive. After the initial playthrough, Missions 1 and 2 will open up for each area. The Mission 1 goal is simple: collect as many medals dropped by the enemies as possible before the end of the level, the aim being to get a high Medal Level. Mission 2 is a bit tougher, but more straightforward; in these missions a set number of enemies must be defeated to achieve rankings. Finally, Mission 3 will open up when you have a C rank or higher in both Mission 1 and Mission 2; these are score based, but have much tougher enemies than found in Mission 2 and, in addition, the player must manually rotate the camera.

Kingdom Hearts II Final Mix adds an extra goal to each mission. For every mission that has successfully been played to S-Rank, hitting Triangle on the controller when selecting these missions unlocks the EX Mission. EX Missions have the same goal as the original, except a restriction or requirement has been placed on the Gummi Ship. Achieving S Rank on these machines earns a bonus Gummi block.

Special Blueprints, which are high-power/high-defense blueprints designed from and made to look like Final Fantasy elements, are usually obtained upon completion of Mission 2 with a rank of S. The Assault of the Dreadnought mission offers models as S-Rank prizes for Missions 1 and 2, and two non-Final Fantasy related blueprints can be obtained by defeating specific enemies on two different routes (a Gold Spider on Asteroid Sweep and the Hunter X).

In addition, receiving 100% on all Gummi Missions for all stages will grant the winner the rare Crown/G Gummi , which enables the ship equipped with it to permanently go into Berserk Mode, a mode which usually relies on reaching Medal Lv30. The drawback is that the ship’s HP is cut down to 1, and cannot be increased.