Unlike the 1980 coin-op classic, which features a nuclear attack from Soviet ICBMs, Missile Command for the Atari VCS takes place in outer space, where Krytolians are out to destroy and seize planet Zardon. Bombers are nowhere in sight, and there is one missile base instead of three. Despite the watered down storyline and a couple of missing elements, basic gameplay remains much the same.

Graphics and sounds are simplified, but not overly so. In fact, when a city explodes, it erupts into a mushroom cloud. In the arcade game, the explosion is circular. The home game includes 34 variations, which effect speed of target control, wave number and intelligence of cruise missiles. There is even a special children's mode of play. Disappointingly, when the game is over, "THE END" does not appear as it does in the original.