Gates of Zendocon is a side-scrolling shooter very similar to the original arcade shooter of this type, Scramble. Unlike Scramble, however, there are 51 game areas in total, but the player fights through a subset of them through branches, choosing the next area to visit.

Some aliens will join you when shot (power-ups). Alien bases in each area allow you to repair your weapons and shield, but landing at the wrong time will cause your ship to explode and lose all power-ups.