Sonic the Hedgehog (2006) Part 2: Shadow's Story

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In the events after Shadow the Hedgehog, Shadow appeared to have joined G.U.N. His story opens in the midst of a rescue mission of Rouge the Bat, who was sent to retrieve the "Scepter of Darkness" from Eggman's base at White Acropolis, and has not been heard from since. Shadow invaded the base and finds Rouge in the midst of accomplishing her mission. They escaped to the site that was formerly the castle of Soleanna's kings where they were confronted by Dr. Eggman, who attempted to retrieve his stolen property. Eggman's robots swoop down to attack, and in the heat of the battle, the Scepter of Darkness was completely shattered. With the seal destroyed, Mephiles was 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 Shadow's chaos control, flung Shadow and Rouge to a future on the brink of collapse. When they arrived, they were first perplexed, but before long, they found some disturbing answers. Along the way, they found an inactive, dusty E-123 Omega, lying in stand-by mode for hundreds of years for an unknown reason. They discovered that they were 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 created a time warp to the present. Sonic and company go back to their time, except for Shadow, who stayed to confront Mephiles. Upon catching up with Mephiles, he revealed to Shadow that the humans, looking for someone to blame for the destruction of the Earth, saw Shadow responsible for the catastrophe. Shadow was hunted down, defeated, and trapped behind an energy seal. Mephiles tempted Shadow to join him to gain vengeance upon the humans, but Shadow refused, at which point Mephiles transformed into his second form, a more powerful crystalline monster, and the two engaged in battle.

Rouge, in the present, realized that Shadow was alone in the future fighting Mephiles, without a chaos emerald. She searched 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, was rescued by Omega, who gives him the chaos emerald and helped Shadow fight Mephiles. Defeated, Mephiles flees to the present through a time warp and Shadow and Omega follow him to the present. Omega pursued Mephiles, and Shadow finds Rouge, who informed him that Dr. Eggman was apparently searching for him. Shadow concluded that Eggman was 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 was under attack by Silver. Shadow rescued Sonic, who runs away with Princess Elise, and Shadow engages in a fight with Silver. Shadow was able to overcome him by freezing time so Silver couldn't 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, opened 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, emerged, opening Silver's eyes to Mephiles' deception. The Duke of 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 defeated him once again, but Mephiles laughed and told Omega that the reason he can defeat him so easily was because he was built to defeat Shadow later on. Omega refused to acknowledge the truth at first, but after Mephiles escaped 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 Mephiles had 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 attempted to seal him in the new Scepter of Darkness, but it shattered and Mephiles was able to free himself. Mephiles revealed that what worked ten years ago no longer does because he was using Shadow's form. Mephiles used his powers to summon a giant clone army of himself and he attempted, once again, to trick Shadow by convincing him that he was a fool for continuing to protect those who will eventually seal him away. In response, Shadow replied, "If the world chooses to become my enemy, I will fight like I always have!" Shadow then removed his inhibitor rings, and in a huge burst of energy, defeats the Mephiles clones with his allies by his side and the story ends as a cliffhanger.

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