It's been two years since Arnold and Sonya were made into Shockmen. A message from the professor to return to their bodies has them head to his laboratory, but they are ambushed by a mysterious enemy along the way. After narrowly defeating the enemy, they catch a TV news flash announcing the Ryo Empire invasion. They find that the professor has been abducted and set out to rescue him.

Shockman is a side-view action shooter that has eight stages, including Action Stages, where you jump and use special techniques, and side-scrolling Shooting Stages. This game expands on the well-paced story from the previous version and contains cooperative elements like shared life and a powerful Team Shockbeam that can be used during two-player simultaneous play.

Shockman takes about two years after the original Kaizou Choujin Shubibinman. Arnold (Tasuke in the Japanese version) is no longer a student and works as a cook in a local restaurant. Sonya (Kyapiko in Japanese version) remains a student. Since the fall of the Dark Skull, Doc has constantly suspected that another invasion was coming sending Arnold and Sonya on searches for the new invaders although never finding anything. However, one day, after Doc is kidnapped, Arnold and Sonya find out that an alien empire led by Ryo is planning to take over the world. Also, two other villains have appeared with similar powers to Arnold and Sonya. They are dark Shubibinman named Jeeta and Mue. Arnold and Sonya must now rescue Doc, stop Ryo from taking over the world, and avoid being killed by Jeeta and Mue.