Alien Invaders approach the solar system from their interstellar battle platform, named Fortress Balangool. Under the command of the Master Control, named L-Brain, the Invaders defeat Earth's space forces. Only one hero, Captain Commando remains to defeat the alien armada by entering Balangool and fighting through the various sections until reaching Section-Z.

Section-Z is a side-scrolling shooter where the player must travel through the maze that is Balangool. Typically this consists of traveling through a scrolling corridor and reaching the end where a new direction must be chosen. Captain Commando's abilities are shooting directly left or directly right while moving around the screen. Power-ups can be collected by defeated enemies and include; improved lasers, a 3-way cannon and shield, these can be stored until needed. There are also SMS (Special Transmission Shell) power-ups, which require energy to use Energy units, are used to absorb enemy fire. Loss of all energy or running into an enemy or a wall causes death.

Certain sections of Balangool are blocked until a generator can be found and destroyed. There are four different boss creatures that must be defeated when encountered.