The story continues from Sonic X Issue 3, where Sonic and co. are still fighting the battle in Station Square Space Museum with Eggman, along with his new robots, which hold most of Sonic's friends inside them. Sonic is unaware of this and continues to resist Eggman and his attacks. Meanwhile, missiles from the battle at the Space Museum fly towards Angel Island, where Knuckles, who is peering out at Station Square, sees them and almost gets hit by them. Knuckles concludes that Eggman is launching another scheme somewhere in Station Square and flies over to the city to investigate.
Meanwhile, Eggman orders his robots to destroy Sonic, Tails and Amy, and Chris Thorndyke tries to resist Eggman's commands, only to discover that he can't stop his own actions, and ends up electrocuting Sonic and his friends. Chris then tries to think of a way to warn Sonic about the people inside Eggman's robots before he destroys them, injuring him and the others trapped within them. As Sonic prepares to attack one of the robots, Rouge flies in front of him and tells him that he can't destroy them because their friends are trapped inside. Rouge shows Sonic more evidence by pointing to the ground, where Sonic notices "Chris" being written with a laser by the robot that Chris himself is trapped inside. Eggman then proceeds to tell Sonic that his friends are indeed inside the robots and that if Sonic and the others don't surrender the Earth to him, then they would be sorry. Sonic refuses to give in to Eggman's demands, which prompts him to order his robots to engage his "Endgame Scenario".
After Eggman finishes commanding his robots, Sonic gives everyone a new strategy, which is to incapacitate Eggman's robots, but not harm them. Although Sonic and co. try to do this, the robots quickly get the upper hand and begin to mercilessly beat them up. During the chaos, Eggman takes joy in seeing that his plan is going exactly as he hoped it would, at which Decoe comments that it's unusual for his plans to ever succeed. Bocoe then asks Eggman where he acquired all the "green pieces of paper" to buy the parts he needed to build the robots. Eggman answers by saying that he went to the "local purveyor of hardware", where he was convinced that, since humans appeared to think that green slips of paper had some value, anything could be traded for goods and services. When Eggman realized that using rotten cabbage as payment for the parts wouldn't work, he threatened the store clerk with one of his robots, which persuaded the clerk to give Eggman all the parts he needed to build his new robots.
Meanwhile, Sonic and co. continue to receive a beating from Eggman's robots. When Sonic notices a Power Ring rolling in his direction, he reaches for it and absorbs its powers, allowing him to escape the net trap he was caught in before being crushed by a robot. He then saves his allies from the other robots. Chuck Thorndyke, Cream the Rabbit, and Knuckles fly into the Space Museum in the X Tornado. Knuckles jumps from the jet and offers his aid to Sonic and co., who then decide which of the robots they should handle in order to save the people trapped inside them. Sonic tells Tails to steal the device that Eggman is using to control the robots from Eggman himself.
When Sonic and co. try to incapacitate the robots again, they are restrained by them once more. The robots are about to destroy Sonic and co. under Eggman's orders, while Eggman and Tails struggle over the device that controls the robots. Sonic urges Chris not to follow Eggman's commands and, putting all his effort into resisting, Chris succeeds in making the robot he was trapped in hesitate to destroy Sonic, which angers Eggman. Meanwhile, Chuck and Cream rescue Tails, who is being held captive, by sending Cheese inside the robot itself and freeing the President of Eggman's control. Chris then forces the robot he's trapped in to attack the other robots in order to weaken them, which gives Sonic and co. an advantage. Watching his plan fail right before his eyes, Eggman attempts to use one last gambit: order the robots to self-destruct and take Sonic and co. with them. Before Eggman can do this, Tails steals the device from him and throws it to Sonic, who uses it to shut down the robots before destroying the device itself. Eggman then flees the Space Museum, promising Sonic that he would return.
Sonic and co. then leave the Space Museum to be greeted by Scarlet Garcia and a crowd of cheering citizens, with Garcia announcing on the news that Sonic has once again defeated Eggman and no one was hurt in the conflict.
- On the cover, Tails is seen piloting the Tornado 2, when it was actually the X Tornado that appeared in this issue.
- On page 7 of Sonic X Issue 4 (excluding the pages showing advertisements), Eggman mentions an "Endgame Scenario", which could be a reference to Dr. Ivo Robotnik's Endgame Scenario from the Sonic the Hedgehog comics (in issues 46-50), in which Robotnik unleashes a master plan to rid himself of Sonic and the Freedom Fighters once and for all, and proceed to rule the world without further resistance. The situation in Sonic X Issue 4, where Eggman orders his robots to engage his Endgame Scenario, is somewhat similar to the situation(s) shown in Sonic the Hedgehog issues 46-50.