Following Dr. Eggman's disappearance, Shadow was determined to hunt down Eggman and prevent him from launching a counter-attack at any cost. He was aided in his search by Rouge. Rouge quickly found the doctor's location, but anonymously passed that information to the Chaotix Detective Agency in order for them to verify it was Eggman and to bring in Sonic the Hedgehog to help bring Shadow to reason.
The Fate of Dr. Eggman
Approximately a month after the Resistance-Eggman Empire war, Shadow and Rogue found a seemingly amnesiac Dr. Eggman dealing and becoming friendly with Sonic and the Chaotix. After Eggman mentioned Eggman Land however, Team Dark revealed themselves, with Shadow declaring that he would destroy Eggman.
While Shadow was led away from Eggman by Sonic, Rouge was confronted by the Chaotix, who accused her of bringing Shadow here. In her defense, Rouge revealed that she had been managing everything to ensure everyone's well-being. In the meantime, Sonic convinced Shadow to give Eggman a chance to explain himself, seeing as his amnesia had made the doctor a good man. By the time Shadow returned, Rouge stood ready to defend Dr. Eggman as well. However, she let Shadow pass after he revealed that he had talked the matter over with Sonic. As such, instead of eliminating Eggman, Shadow had Eggman show him Eggman Land, which turned out to be an amusement park for children that Eggman had made. Convinced that Eggman was now a good man who deserved to be forgiven and live in peace, Team Dark took their leave.
The Battle for Angel Island
Shadow and Rouge were later called in to aid the Rsistance at a meeting in Resistance HQ. There, the Resistance's members revealed that Neo Metal Sonic had taken over Angel Island and turned it into a flying fortress. To make matters worse, Neo had also secured the Master Emerald for himself on the island. With their goal being to liberate Angel Island, Amy Rose came up with a strategy after some internal discussions: team three (Sonic and Knuckles) would confront Neo and secure the Master Emerald while team one (Blaze) and team two (Shadow, Rouge and everyone else) focused on breaking the Egg Fleet's control over the island. On the way to Angel Island however, the heroes' battleship came under fire from the Egg Fleet. Fortunately, everyone got off the ship before it crashed. While team two began their mission, Blaze became Burning Blazs and began her attack on the Egg Fleet. Meanwhile, team three confronted Neo Metal Sonic inside his fortress on the island.
Unsatisfied with his part in the plan, Shadow split off from team two, leaving Rouge to make up for his absence and start taking direct orders from Amy and handle the guns of the ship they were attacking. Whilst Rouge aided in the take-over of one of Eggman's ships and saved the life of Amy, Shadow eventually met up with team three and went into a direct confrontation with Super Neo Metal Sonic, knocking him out of his Super State and seemingly besting him. This proved to be in error, though, as Neo Metal Sonic copied Shadow's bio-data and used it to complete his transformation into Master Overlord. After a brief scuffle, Master Overlord grabbed Shadow, Sonic and Knuckles and flew off with them so they could see him destroy their allies, who had sought refuge onboard an Egg Fleet battleship. When Master Overlord approached the battleship however, Shadow escaped his grasp alongside Sonic and Knuckles, and began destroying his wings to drive the giant robot back towards the now-freefalling Angel Island, all while Knuckles tried to retrieve the Master Emerald from Master Overlord. Rouge soon after also joined the fray. During the battle, Team Dark got shaken off Master Overlord, but were rescued by Silver with his psychokinesis. Knuckles subsequently got the Master Emerald away from Master Overlord and brought it back to Angel Island, returning the island to the sky while Master Overlord powered down to normal. With the battle over, Team Dark's members were brought down to Angel Island where they parted ways again.
- ↑ 1.0 1.1 1.2 Sonic the Hedgehog #9, Roll Call
- ↑ 2.0 2.1 Sonic the Hedgehog #6, "The Fate of Dr. Eggman Part 2"
- ↑ Sonic the Hedgehog #5, "The Fate of Dr. Eggman Part 1"
- ↑ 4.0 4.1 Sonic the Hedgehog #9, "The Battle for Angel Island Part 1"
- ↑ 5.0 5.1 5.2 Sonic the Hedgehog #10, "The Battle for Angel Island Part 2"
- ↑ Sonic the Hedgehog #11, "The Battle for Angel Island Part 3"