Commander Keen's newly finished homemade faster-than-light radio picks up a plot by the Shikadi to destroy the galaxy. He rushes to the planet Gnosticus IV to consult the Keepers of the Oracle, but discovers that they have been taken captive. Thus, the gameplay centers on Keen finding and rescuing the eight elders. This episode features huge levels and a wide variety of enemies, such as rocks that only move when Keen's back is turned, and modified game mechanics. The game also features a mini-game called "Paddle War", a remake of the video game Pong, though this version is vertical instead of horizontal.