- Coinciding with the eagerly awaited Shadow the Hedgehog video game from Sega, it's the eagerly awaited return of Sonic's dark counterpart, Shadow! After the huge fan response to the earth-shattering events in issues #146-149, Shadow returns to his mission of learning the truth of his hidden past... even if he has to destroy Sonic and the evil Dr. Robotnik to get it! This time, however, a bigger unknown threat lurks in the background, waiting to destroy them all! One of the biggest, boldest twists ever to hit the Sonic comic-verse happens here!
On an island abandoned by the Station Square military, Shadow approaches a facility known as Laboratory Zero after spending weeks gathering information about his origins. The black Hedgehog questions why he is drawn to the place, but recognizes that he is somehow connected to it. Smashing through a wall to get inside, he questions who would have built the place, but then hears a voice from nearby. He then discovers a room where a video monitor is playing a video recording of Gerald Robotnik as a new version of Metal Sonic stands by. Gerald's recording states that Station Square wished to use his creations for their own purposes, but also that he decided to use them to avenge Maria Robotnik's death. Astonished by the apparent revelation of his purpose, Shadow is then attacked by Metal Sonic and thrown into a emergency container. Recovering a blaster from among the broken glass, he briefly considers using it before tossing it aside to engage Metal Sonic hand to hand. Metal Sonic admits to understanding why its predecessor didn't survive an encounter with Shadow, before boasting of its own superior systems. It then blasts Shadow with liquid nitrogen from a nearby pipe, but Shadow evades the attack and uses high voltage power cables to electrocute his foe. As Metal Sonic falls and recovers the blaster, Gerald's recording reports that the Eclipse Cannon will soon be ready for activation, while another voice then states that he is to be executed. As Gerald vows that his vengeance will not be stopped, Metal Sonic takes aim at Shadow, who hurls a rock into the blaster's barrel. The explosion knocks both unconscious, and they are then found by Mecha, who is intrigued by Shadow's presence and takes both with her, remarking that Eggman will undoubtedly deal with Metal Sonic if he damaged the data he was sent to retrieve.
An alarm in New Megaopolis awakens Dr. Eggman, who groggily heads for his control room as the alarms continue to blare. He complains bitterly regarding his organic form, but is soon distracted by a message on his main monitor: that later that day, he "will undergo a System Shutdown." Calling upon A.D.A.M., Eggman has him turn off the alarms and analyze the message, only for A.D.A.M. to report that he cannot determine the signal's origin and that unless something is done, he will soon be the least of Sonic's problems. Meanwhile, at Sonic's house in Knothole, the Hedgehog is up late playing music on his guitar and singing, to his mother Bernie's distress. Going back to her room, she speaks with her husband, both of them agreeing that Sonic misses Sally despite his relationship with Fiona. Jules suggests talking to him, but Bernie feels that Sonic and Sally must work out things without interference. Jules then remarks that it would be good if Sonic had something besides the war to occupy his attention.
Back in New Megaopolis, Eggman decides to try and identify his enemy by process of elimination. A.D.A.M. suggests Snively as the most likely candidate, though Eggman also feels that King Max, Sally, or even Knuckles might be responsible. A.D.A.M. then suggest taking preemptive action to draw his enemy into the open, which Eggman considers. Later, Rosie and Hope are out hanging laundry and discussing plans for that day when a shadow falls over them. Sonic, in something of a bad mood, is then startled by the same shadow, the source of which he quickly identifies as an Egg-shaped object descending from the sky. It turns out to be one of Robotnik's ships, and as it lands Eggman himself apparently disembarks. The confused and scared citizens of Knothole-including Rotor and Tails-consider what they should do, with Rotor deciding that they should treat him as a visitor unless he takes any hostile action. Elsewhere, Sonic is about to rush out to meet the threat, but is stopped by his mother, who demands that he have some breakfast before he leaves. After a brief discourse, Sonic finally reveals that he spotted the ship landing, and his mother lets him go with a word of caution. Sonic then opens his front door to find Eggman standing outside, wondering if he was "expecting maybe Princess Sally or one of your other girlfriends?" Sonic then attacks, only for Eggman to dodge him. The two then engage in a brief tussle, with Eggman displaying speed and strength far beyond what he has shown before. Sonic then lands a kick and is able to pass through his foe, revealing Eggman as a hologram rendered solid by a device that Sonic has now destroyed. Eggman then gets down to business, stating that he is here to ensure his own survival, to the disbelief of the Hedgehog family.
Eggman then reveals the apparent time limit on his existence, prompting Jules to question why Sonic has anything to do with this. The doctor is quick to insult the Robian and make a gibe at his brother Charles, but then reveals that given Sonic's ability to make him miserable, he had hoped that Sonic would be able to similarly persecute his enemy. Jules further questions why they should get involved, and Eggman gives them two reasons: they're familiar with him as opposed to whoever is threatening him, and he claims that he can restore Jules to normal. Rotor and Sonic then board the ship and head for New Megaopolis, where Eggman welcomes them before receiving another System Shutdown notification. Eggman then explains that he believes that his foe revealed itself in part some time ago, with the demonstration of a technology that he no longer thought was possible. They then hear the sound of a robot approaching, prompting Sonic to accuse Eggman of luring them to the city, though Eggman is quick to say that he doesn't think the robot is one of his. Mecha than breaks into the room, surprising Sonic after her apparent demise in their last encounter. Mecha then confronts Eggman, but Sonic lassos her only to be tossed aside. Mecha then reveals that Eggman is to pay for his crimes against the Kingdom of Acorn, and that the message he received had a twelve hour delay, meaning that his time is already up. Doors to the room then open to admit several Metal Sonic Troopers, and Mecha reveals that "My master in now in control!"
- Shadow learns that he was designed as a weapon by Professor Gerald.
- Shadow and Metal Sonic fight, which results in both being rendered unconscious.
- Mecha collects both Shadow and Metal Sonic, bringing them to Dr. Eggman.
- Shadow's pose on the cover is based on a piece of artwork from the game Shadow the Hedgehog, only without the gun.
- This issue cover is one of the six in the main Sonic comic series to not feature Sonic in the art, the others being StH: #15, #146, #190, #210, and #240. (Due to SEGA, Sonic was on the covers in some form, be it an icon, corner box or an alternate form.)