When Station Square's chaos emerald is stolen by a super fast hedgehog, Sigma Alpha-2 goes searching for the most likely culprit...Sonic the Hedgehog.
As the Shadow Awakes
The military comes to ARK to take over Project Codename: Shadow.
Sonic Adventure 2
Three months ago, Doctor Eggman was being chased by his Silver Sonic II after it was reprogrammed by Nate Morgan to protect Station Square. Eggman is chased all the way to Prison Island and falls through the floor, supposedly to his death. He instead fell into a closed prison/lab and, upon inspection of a data log, finds it belonged to his grandfather Gerald Robotnik and contains new weapons for Eggman to try out.
One week ago, Shadow the Hedgehog steals a Chaos Emerald from a Station Square bank. Silver Sonic tries to stop him but is easily destroyed. Detective J.J. Moto is given the case, who gives the president the bank's security films. The president recognizes Shadow as Sonic and hires Rouge the Bat to recover the emerald.
24 hours ago, a team of GUN operatives leave Station Square and capture Sonic the Hedgehog with an electric net. In the helicopter to Station Square, Sonic notices a loose screw. He takes out most of the crew and busts out mid-flight. Using a piece of the helicopter as a board he slides into the city and escapes briefly only to find himself being chased by a large GUN truck.
As the Shadow Awakes
Some time ago, Dr. Gerald Robotnik is trying to unlock the secrets of immortality in the space station ARK. He talks half to himself, half to a creature in a tube. There is a power surge and Gerald expresses excitement in realizing the creature in the tube lives. His granddaughter Maria appears on a screen, asking what happened and to tell him that a space shuttle from Station Square is coming towards them. Gerald orders Maria to come to him. The shuttle docks and the military boards, attempting to retrieve "Project: Shadow" from Gerald, as he doesn't believe the military should have it. Gerald tries to stall the men while Maria and Shadow escape in a pod. Shadow gets in but Maria—a young, crippled girl—is shot in the back by the military. Shadow and his pod escapes.
Gerald is taken to a prison/lab on Prison Island and is forced to make another Shadow. The original Shadow's pod washes ashore but is empty. Angry at his granddaughter's death, Gerald plots his revenge. He built a laser cannon in the ARK strong enough to destroy planets. Shadow has a piece of Gerald's DNA in him so that, should he die, Shadow will make his revenge. Robotnik also makes a chip detailing his plans and hides it in the lab. Worried Gerald is pulling a fast one, the Station Square military pulls the plug on the project and has Gerald executed. The chip remains hidden.
Spike: -go to?
Sonic: (while holding their guns in his arms) Wouldn't it be better to ask "What happened to our guns?" instead?
Sonic: (after escaping the chopper) *thinking* Talk about low-budget flights—no food or movies. I'm outta here! 'sides...I'd feel better running!
First appearance of Shadow
First appearance of Rouge
This issue is the first appearance of Rouge even though the Sonic Comic Encyclopedia says her first appearance is issue 99 shes not even in issue 99
The scene where Sonic breaks out of the GUN helicopter is a word-for-word recreation of the same scene in Sonic Adventure 2, albeit with a few extra bits of dialogue added in.