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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. Differences between the NES and FDS are that in the FDS version you can save your game in three slots and begin again from where you left off.