Why is Superman trying to arrest the Flash? What could possibly have happened to turn the Man of Steel against the Crimson Comet?
The Flash, in pursuit of a lightning-like energy pattern, is drawn into an inter-dimensional vortex. Clark Kent, Jimmy Olsen, and Lana Lang are on a cruise through the Florida Keys. Kent receives the Flash's distress signal, via his Justice League of America communicator. Kent, as Superman, immediately responds to the Flash's signal. En route, Superman mulls over the troubles ailing the Scarlet Speedster. The Flash had been forced to kill his nemesis, Professor Zoom, to prevent the Reverse Flash from murdering the Flash's bride-to-be, Fiona Webb. The Flash was indicted for manslaughter, and only Superman had been able to keep the Flash from being ousted from the ranks of the Justice League of America. With the Flash's trial ongoing, Superman wonders what new problem could the Flash be facing. Superman follows the Flash's signal to the vortex, and flies inside. Superman finds himself flying over a vast ocean of molten lava, with a single floating city hovering above it. Flying through the city, Superman finds portions of it completely destroyed. Unbeknownst to Superman, his movements are being observed by four Kryptonian villains, trapped within the Phantom Zone, Faora Hu-El, General Zod, Jax-Ur, and Kru-El. Superman is attacked by the denizens of the city, called "Norkkans". Their violent actions are in response to the earlier arrival of the Flash. It seems the Scarlet Speedster is the culprit behind the destruction of their city. Superman refuses to believe that his friend would behave in such a wanton, destructive manner. Then, the Flash appears, using his super-speed abilities to bring down another tower. Superman vaporizes the falling debris with his heat vision, then grabs the Flash. The Scarlet Speedster vibrates out of Superman's grip, then races away.
The Phantom Zone villains are revealed to have engineered the entire situation. Exerting psychic influence over the Norkkans, the Phantom Zone villains first bade them to transmit the energy phenomena to Earth, which lured the Flash to the vortex. The Flash's distress call summoned the Phantom Zone villains' true target, Superman. With the Flash under their mental control, the Phantom Zone villains now exert their influence over the Norkkans, pushing them to complete their work on an inter-dimensional injector cannon. The Phantom Zone villains are on a tight schedule, as the atmospheric phenomena that has allowed them to influence the Norkkans is beginning to dissipate. The Norkkans finish building the injector cannon. With no further use for the Flash, Faora Hu-El merely instructs him to decelerate as he races across the surface of the molten ocean. The Scarlet Speedster is consumed by the burning lava. With Superman in the sights of the injector cannon, Jax-Ur gives the command to fire. The Norkkan's strong sense of morality keeps him from pulling the trigger. The other Phantom Zone villains combine their psychic power with Jax-Ur, pushing the Norkkan over the edge. The cannon is fired. The Flash, having saved himself by vibrating his molecules into intangibility, bursts up from the lava sea. Outracing the cannon blast, the Flash takes the shot intended for Superman. Immediately, the Flash finds himself transported into the Phantom Zone. The injector cannon, however, was attuned to Superman's unique Kryptonian physiology. As the Flash is human, the injector cannon's beam is not able to hold the Flash in the Phantom Zone. In short order, the Flash returns to the world of the Norkkans, then returns to Earth, with Superman.