In six hours the evil Professor Elvin Atombender's nuclear missiles will launch and destroy strategic locations on the earth. Only one agent can infiltrate his secret base and undertake this Impossible Mission.

The goal of Impossible Mission is to acquire nine passwords and bring these to Atombender's Control Room in time to shut down the rockets. Unfortunately these passcodes (contained on punch cards) have been broken into four pieces each, and each piece hidden in computers, furniture, and waste bins throughout the base. On top of that Atombender has an entire army of robots patrolling the base. If a robot touches or shocks the agent then ten minutes are removed from the clock and the room is reset. The agent can jump over robots, but the only way to stop them is to expend a specific item on a room's computer terminal, and even that only disables them for a few seconds.

The 2007 release of the game has a few improvements over the original version, mostly to improve the graphics and make the game easier. The player can select one of three agents, although all of them possess the same abilities. Robots are now color coded according to what they are capable of doing (yellow only patrol, red patrol and shock, blue can follow and shock), but some aspects of each robot's personality can still only be figured out by watching or approaching them. Finally an easy mode has been added that adds an extra two hours to the clock and marks rooms which you have cleared out of items. The original mode with the original graphics can also be played, as well as a "mixed" mode that uses the old avatar graphics, makes all robots the same color, but keeps any other graphical upgrades.