Dr Robotnik has been reduced to total insanity. Every day in the asylum, he merely stands in his cell, staring out at the world, seldom sleeping, never talking. One day, without warning, his cell is blasted open from the inside. Someone has come to collect him. Shortly afterwards, Sonic and Tails are in hot pursuit in the Bi-plane. What they believe to be a storm slowing them down is revealed to be the turbine of a massive flying fortress. After trying to land, and losing the Bi-plane in the process, they begin to explore the ship, and are fired upon from the shadows. Tails opens a deck door, but is knocked out and separated from Sonic before the hedgehog can get to him. Sonic tries to follow Tails' attacker, but sets off an alarm and is soon being chased down by a mysterious muscle-bound Echidna in a modified Egg-o-Matic bristling with weapons. The hedgehog dodges the attacks, but lands on a weak part of the floor which collapses beneath him. When he comes around, a strange ring has been placed on his leg, and he is faced with doll replicas of him and his friends. Suddenly, the voice of Doctor Zachary booms over the speaker system, welcoming Sonic to the Death Carrier and making special note of his imminent death.
Robotnik emerges and begins to fire upon Sonic, Zachary warning Sonic that the Tracking Ring on his leg will make him easy to find, and electrocute him should he try to attack Robotnik. As Sonic flees, Zachary, observing the proceedings, recieves a communication from his new ally, the muscle-bound Vichama, who is watching over Tails, who is in a tank slowly filling with water. Vichama wants to know why Sonic can't just be instantly electrocuted, but Zachary states that they need the hedgehog alive for the moment. Sonic meanwhile has found the ventilation system, and is attacked by a Badnik. He breaks a part off the Badnik, uses it to snap off the Tracking Ring, and continues his search for Tails, fighting off every Badnik and trap he comes across. He soon finds himself in what seems to be a break room, where he is met by the friendly robotic guide Omochao. Omochao happily points Sonic in the right direction to find Tails, before being eaten by a Rexon, as the Badniks track Sonic down. Sonic quickly breaks Tails out of his watery prison before they are attacked by more Badniks and Robotnik again. Before they can be completely overwhelmed however, Sonic finds a hydraulic pump which releases water from the ship. He grabs Tails and flees on a flying scooter of sorts. Robotnik can wait: Saving a friend is more important to Sonic for now. The Syndicate however have completed their mission for the day. As opposed to killing Sonic, they sought samples of his DNA, which they obtained thanks to the Tracking Ring. Today, they have completed a project started by the Drakon Empire, and Vichama and Zachary gaze upon the soon-to-be awakened ultimate life form: Shadow the Hedgehog.
- Vermin the Cybernik and Fleabyte are shown to be in the cells next to Robotnik's.
- Shadow's big reveal is somewhat spoiled by the end of the first part of the story, as he is visible on one of the monitors in The Syndicate's crowd shot.
- Rouge clearly moves quickly, as the monitors in the second part show she is already in the Haunted Hill Zone, leading into the upcoming Knuckles The Echidna storyline.
- The Marxio Brothers' video games, briefly mentioned in The Sonic Terminator, are on show here, in the form of GameCube exclusives Super Marxio Sunshine and Chicio's Mansion.
- The cabinets in the Death Carrier's break room contain several artifacts from Sonic the Comic and the games, including Shortfuse the Cybernik's helmet, a Metallix head, a Drakon Prosecutor helmet, a few Badnik heads, what appears to be a Golden Nose of Robotnik, and a Chao in a jar (it's not certain if the Chao is alive or not).