Sonic has come to visit Porker Lewis on the Floating Island, the Emerald Chamber still a mess after Knuckles the Echidna had a battle with the head of a Guardian Robot. Sonic generally wonders how Porker is doing and the pair joke about Amy Rose. Suddenly, the robot head recognises intruders and shouts. This surprise, combined with the unstable masonry around the Chaos Emeralds causes Sonic to fall into the Chaos Energy. Aware that all the energy must affect Sonic badly, Porker hides and, sure enough, an enraged Super Sonic climbs out of the shaft. Wanting something to destroy, he remembers talking about Amy and bursts out of the room to find her. On his route, he crashes straight through a warship filled with Trooper Badniks. On the surface, Amy is teaching Tails how to fire a crossbow in case something happens to her when Johnny Lightfoot comes running. Porker has sent an urgent message, but before Johnny can pass on the news, Super Sonic has found them and is ready to kill Amy.
Super charges at Amy but misses and ploughs into Bob Beaky's Travelling Circus caravan, destroying it. He doesn't emerge from the inferno straight away, worrying Johnny, but Super comes out alive, mad as ever. Super unleashes his new eye-beams, causing devastation to the Freedom Fighters. He takes another dive but misses, ploughing straight into a cliff, which then collapses on him. Fortunately, and unfortunately, Super is still alive. Johnny suggests Tails should fly and fetch Knuckles, but Tails refuses. However, it gives Amy an idea and they find their biplane undamaged. Super follows them and sees the plane flying. Had enough with the games, he shoots the plane down. Super maniacally cackles at his destruction around him, until he turns back into Sonic. He looks at the devastation and is distraught.
At Spike's Place, a dangerous bar in the Metropolis Zone, some regulars are talking about the recent events. A hooded character makes a snide comment and when one of the barflies removes the character's hood, it is revealed to be Sonic. As they all move in to capture Sonic and receive the reward from Doctor Robotnik, the stress gets to the hedgehog and he turns back to Super, trashing the bar. The Freedom Fighters, still alive, are tracing Sonic using the Kintobor Computer when Super smashes out of the bar. Amy reveals she remotely used Kintobor to fly the plane and tries to convince Super to revert back to Sonic. It doesn't work and he dives at her. Luckily, Tails and Johnny have removed the cover off a Star Post. Amy connects a line between it and Kintobor. The Star Post suddenly locks on to Super as he chases after Tails. As it drags him back, Super tries everything to pull free but is eventually sucked into the Post. Moments later, Sonic returns from it, his usual self. Amy reveals Kintobor removed all of Sonic's radiation, but the computer reveals that Super may still be alive in the Special Zone, surviving without Sonic.
- Running Wild is often regarded as one of the best stories in Sonic the Comic by the fanbase.
- This story saw Super separated from Sonic for the first time. He wouldn't be reunited in the same body until the final story, Point of No Return!.
- Nigel Kitching's original title for this story was "The Fury".