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After the great battle in which the evil Baron Karza was destroyed and unfortunately all life on the planet Homeworld was eradicated as a result, the Micronauts set out to find new adventures. But they were thrown far, far off course, way beyond the Microverse. They met a strange alien life-form, and Scion joined them aboard their ship, the Endeavor. In fact, they were thrown far enough away that they could see that the whole Microverse looked like one giant DNA Spiral, the molecule that controls life.
But it turned out that one of their friends, named Devil, who had stayed behind on Homeworld, was being chased by a mysterious danger. He escaped by a teleport-beam, but something went wrong. The beam was twisted somehow so Devil couldn't reform, so they stored his matrix inside Biotron, one of the Roboid Micronauts. They decided to go back to Homeworld and try to help Devil get back his body.
But something was very wrong, as they tried to get through the spacewall that surrounds the Microverse, the Enigma Force (the very power that keeps the Microverse together) attacked them. A giant time traveller appeared to prevent them from getting back to the Microverse. Scion finally figured out a way to get them back across the spacewall, but the whole Microverse seemed to be in trouble.
The Micronauts finally made it to Aegis, where the refugees that fled the awful something were gathered, and there the Micronauts stopped and waited.
Note: Marvel no longer has the rights to the name, so the team is renamed The Enigma Force in newer stories.