A space shuttle heading for the Joes' Space Station Delta is attacked by Cobra. While the Joes are distracted, Cobra plants several cargo boxes aboard the shuttle. Cobra retreats and the Shuttle launches. The Crimson Twins and Cobra Commander are nearly captured but escape with the aid of the Water Robots. Destro is chased through Enterprise City by the Joes in Skystrikers but enters a skyscraper from a secret entrance.
Meanwhile, the Joes notice that the shuttle is too heavy and find the extra cargo. They dock on Delta and open the boxes. Inside they find small, cuddly creatures called Fatal Fluffies and a card from Cobra Commander. Zartan, disguised as a Joe, has also sneaked aboard the shuttle as have the Dreadnoks. Zartan blows a whistle, turning the Fatal Fluffies into big, bad monsters with laser pistols. After being unable to contact Delta, Joe HQ finally receives a transmission from them. That allows Zartan to lock on to the location of Joe HQ and blast it with energy cannon from Delta. Joe HQ is nearly destroyed. Controlling Space Station Delta is the first step in Cobra's plan to create a pyramid of darkness. Next, they have to position the control cubes on the four corners of the earth.
Under the river, the Sharc encounter the Water Robots, Shipwreck and Snake Eyes are both hit but make their way to the underwater Cobra base and sneak inside. They find a Cobra subway that leads to a Cobra assembly plant. However, at the gate, Shipwreck fails the voice identification and the group is nearly cut and smashed to pieces.