Sonic Heroes storyEdit
Rouge had heard Dr. Eggman had a vast treasure, so she infiltrated one of his bases. When she entered one of the rooms, she found Shadow in a stasis container. She set him free of the stasis, but (accidentally) activated Omega too. Due to the anger of being locked up, Omega attempted to destroy Shadow, thinking he was an Eggman robot. After she stopped the two from killing each other, She had been told a few things on both sides: Omega was the last of Eggman's E-100 series robots built to guard and contain Shadow, should he get free. Shadow had amnesia from falling from the Space Colony ARK (indirectly alludes to Sonic Adventure 2, as the ARK was not mentioned in this scene). Rouge decided to make the two(and herself) into a team. Gameplay starts from there.
After Team Dark completes the Power Plant zone, they encounter Team Chaotix, whom Rouge mistakes are looking for Dr. Eggman's treasure, too, leading to the two teams battling. Later, when Team Dark defeats the Egg Albatross, the Eggman they were battling turned out to be a fake. Then, Shadow sees a destroyed Shadow Android, and begins to wonder if he, too, is an android. At Frog Forest, they encounter Team Sonic, who are surprised to see Shadow still alive. The two teams then battle. After a final showdown with Dr. Eggman, Rouge looks for Eggman's treasure, but instead finds an enitre room of immobile Shadow Androids. Rouge tells Omega that the Shadow they teamed up with was a clone, and Omega cheers her up by telling her that for there to be clones, there has to be an original, meaning that Shadow could still be alive somewhere. Team Dark assist Team Sonic and the others teams to defeat Metal Overlord in the Final Story of Sonic Heroes. Rouge runs off to find the Master Emerald, where Shadow and Omega stay behind, with Omega cradling the deactivated body of Metal Sonic.
Sonic Next Gen Edit
Team Dark's story opens in the midst of Shadow's rescue mission of Rouge the Bat, who was sent to retrieve the "Scepter of Darkness" from Eggman's base, and had not been heard from since. Shadow invades the base and finds Rouge in the midst of accomplishing her mission. They escape to the site that was formerly the castle of Soleanna's kings where they are confronted by Dr. Eggman, who attempts to retrieve his stolen property. Eggman's robots swoop down to attack, and in the heat of the battle, the Scepter of Darkness is completely shattered. With the seal crashed, Mephiles is freed.
Resurrected in the likeness of Shadow through his shade, Mephiles the Dark introduces himself and hints at past history that the two shared. Mephiles, using a time warp, similar to Chaos Control, flings Shadow and Rouge to a future on the brink of collapse. When they arrive, they are first perplexed, but before long, they find some disturbing answers. Along the way, they find an inactive, dusty E-123 Omega, lying in stand-by mode for hundreds of years for an unknown reason. They discover that they are in the distant future, destroyed by the demon Iblis. Shadow and Rouge meet up with Sonic, Tails, and Knuckles, who were sent to the future by Eggman's latest machine. Sonic and Shadow conclude that they must use Chaos Control to get home, and set out to locate the Chaos Emeralds. After a confrontation with Iblis, they succeed in finding two Chaos Emeralds and successfully create a time warp to the present. Sonic and company go back to their time, except for Shadow, who stays to confront Mephiles. Upon catching up with Mephiles, he reveals to Shadow that the humans, looking for someone to blame for the destruction of the Earth, saw Shadow responsible for the catastrophe. Shadow is hunted down, defeated, and trapped behind an energy seal. Mephiles tempts Shadow to join him to gain vengeance upon the humans, but Shadow refuses, at which point Mephiles transforms into his second form, a more powerful crystalline monster, and the two engage in battle.
Rouge, in the present, realizes that Shadow is alone in the future fighting Mephiles, without a Chaos Emerald. She searches for E-123 Omega, gives him a Chaos Emerald, and tells him to sit and wait in stand-by mode until the distant future becomes the present, and to assist Shadow fighting Mephiles. Shadow, at Mephiles' mercy, is rescued by Omega, who gives him the Chaos Emerald and helps Shadow fight Mephiles. Defeated, Mephiles flees to the present through a time warp and Shadow and Omega follow him to the present. Omega pursues Mephiles, and Shadow finds Rouge, who informs him that Dr. Eggman is apparently searching for him. Shadow concludes that Eggman is searching for Mephiles, and goes to interview the doctor. Upon locating Eggman's base, Eggman tells him that, to understand why he wants Mephiles, Shadow must know about the accident that happened 10 years ago, the Solaris Project.
Shadow then leaves only to find Sonic, who is under attack by Silver. Shadow rescues Sonic, who runs away with Princess Elise, and Shadow engages in a fight with Silver. Shadow is able to overcome him by freezing time so Silver cannot defend himself. Refusing to just be defeated, Silver also induces Chaos Control, to Shadow's shock. Shadow tells Silver that in order to understand more about Mephiles and Iblis, they would have to use the warp and witness the accident themselves. So the two of them, using the Emeralds, open a time warp to 10 years ago, the Solaris Project. They witness the Solaris Project's failure at hand, and watch as Iblis and the original Mephiles, a dark puddle, emerge, opening Silver's eyes to Mephiles' deception. Duke Soleanna tells them that the demons must be sealed, so he gives Shadow the Scepter of Darkness. Shadow goes to capture Mephiles, and Silver goes to capture Iblis. It is here that Shadow finds out why Mephiles knows him; it was Shadow who sealed him in the Scepter of Darkness in the first place. With the demons sealed, Shadow leaves the Scepter in the past since he knew where it would end up in the present day. Silver and Shadow return and Shadow rushes off to find Rouge to tell her what he learned about Mephiles. Shadow finds Rouge, and tells her to find out what the Scepter of Darkness, Mephiles' seal, was made of, so they can create another one.
Elsewhere, Omega has found Mephiles on the beach and defeats him once again, but Mephiles laughs and tells Omega that the reason he can defeat him so easily is because he was built to defeat Shadow later on. Omega refuses to acknowledge the truth at first but after Mephiles escapes again he admits to Shadow and Rouge that he was the one that sealed Shadow in the future. Shadow, Omega, and Rouge chase Mephiles to a desert temple with a new Scepter of Darkness, but the evil Mephiles has already found the yellow Chaos Emerald. After Shadow fights him and gains victory, Mephiles reverts back into his original form, a puddle of darkness. Shadow attempts to seal him in the new Scepter of Darkness, but it shatters and Mephiles is able to free himself. Mephiles reveals that what worked ten years ago no longer does because he is using Shadow's form. Mephiles uses his powers to summon a giant clone army of himself and he attempts, once again, to trick Shadow by convincing him that he is a fool for continuing to protect those who will eventually seal him away. In response, Shadow replies, "If the world chooses to become my enemy, I will fight like I always have!" Mirroring a similar ability from Sonic X, Shadow removes his power rings, and, in a huge burst of energy, defeats the Mephiles clones with his allies and the story ends as a cliffhanger.