Like its predecessor, Space Harrier II is an entirely linear game. The only difference this time around, is that you are allowed to pick any of the twelve regular stages to be your starting stage. Once you do this, you must proceed from that stage to the next by reaching and defeating the boss of each stage in a fixed order.
The order in which you face the stages is prescribed. If you did not pick Stuna Area as your first stage, then you will roll around to it after you defeat Hot Palace. Once you have completed all twelve stages, you advance to the thirteenth and final stage. You are also treated to a bonus stage every time you complete five normal stages.
Each stage of Space Harrier is "on rails" and proceeds in a predetermined fashion. While you have the ability to weave left and right in order to dodge terrain, it is impossible to alter the order with which you encounter the various enemies in the stage.
After the fourth stage that you complete, and after the eighth stage that you complete, you will be treated to a bonus stage. On this stage, you will hop on top of some type of hover board. Throughout this stage, you will be invincible. Enemies will not shoot at you, and any enemy or obstacle that you collide with will be destroyed. The object of the bonus stage is to shoot or collide with as many obstacles or enemies as possible. A tally will be kept of how many objects you've destroyed. When the stage is complete, you will be rewarded with bonus points for every object you destroyed. Then you will immediately move on to the next stage of the game.