Earthworm Jim 3D starts with Earthworm Jim getting squashed by a cow, leaving him dazed and confused. In the aftermath, his marbles go missing, so he must travel into his brain to find them and put everything right again.
The gameplay of Earthworm Jim 3D is similar to that of the previous titles but takes place in a 3D environment. Players control Earthworm Jim as he navigates through various levels, collects power-ups, and fights against enemies.