Mission Alphatron is a variant of Scramble. Like in the arcade game the player controls a spaceship through a side scrolling cavern blasting everything in it's way. The ship has two weapons: a laser that can destroy anything that is in front of it and bombs that can be dropped on ground installations. There are several different types of enemies including rockets, missiles, mines and fighters. Fuel is limited and can be replenished by shooting one of the many fuel tanks scattered throughout the game. If it runs out the ship will explode. Other installations such as buildings and radar stations can also be destroyed The player has three lives and when they are gone the game is over. Bombs can only be used in the original MTX release. In later ports only the laser is available.