Mephiles the Dark is the primary villain of the 2006 Sonic the Hedgehog video game. He was accidently created during the Solaris Project. After he escapes in an formless ooze, he is sealed in the Scepter of Darkness by Shadow the Hedgehog, who traveled through time to ten years before the events of the 2006 Sonic game. In the present, Dr. Eggman accidently releases him while trying to steal the scepter from Shadow and Rouge the Bat, and runs away scared, not even bothering to send his robots to attack him. Mephiles then transforms into his Shadow the Hedgehog form, and sends Shadow and Rouge into the future after he realizes that Shadow doesn't know who he is.

To accomplish this, he tells Silver the Hedgehog and Blaze the Cat that Sonic the Hedgehog was the cause of Iblis being released, which led to the destruction of their world. Sonic was, thus, referred to as the "Iblis Trigger". He sends the two back in time, making them believe that killing Sonic would save the future.

Mephiles even tells Shadow that the world, and eventually Omega, will betray him in the future, and asks him to join him in order to punish the world of humanity. Shadow, however, refused to believe and join Mephiles, and fights him, while Omega aids Shadow. Mephiles retreats to the present, and somehow transforms back into his Shadow form in order to keep manipulating Silver and Blaze. He tells them that Sonic is at the terminal station, and it's now or never if they want their world to be safe. Later, he encounters Omega, who starts to shoot him. After getting shot, Mephiles reveals that Omega himself was created to defeat Shadow in the future. Enraged by this, Omega swithes to his machine guns, and shoots Mephiles again. As Mephiles started to fade away, he laughs evily. After Omega told Shadow about Mephiles' statement, Shadow feels hurt and walks away. Meanwhile, Shadow, Omega, and Rouge encounter Mephiles once again, and fight him. After they defeated him, Shadow tried to imprison Mephiles with their new Scepter of Darkness, but Mephiles proved to be immune to be imprisoned and pushes Shadow, and his partners away. He then uses two Chaos Emeralds to create clones of himself. He then boasts to Shadow that he can't defeat him, and asks why he is even bothering to protect a world that will eventually turn against him. Shadow responds by saying, "If the whole world decides to become my enemy, then I will fight like I always have", and he and his "amigo" partners defeat the entire army.

Mephiles kills Sonic

Mephiles killing Sonic with a Dark Chaos Lance.

After either Mephiles escaped or survived the battle with Shadow, he finds the purple Chaos Emerald, uses it to warp to Sonic and Elise's location shortly after they escape Eggman's exploding Egg Carrier, blinds them with the Emerald's powers, and impales Sonic through the back with an energy beam, killing him instantly. Elise cries over his death and, as a result, releases Iblis, allowing Mephiles to fuse with him and transform into Solaris. It is also revealed in the Last Story that his lie to Silver and Blaze about Sonic being the Iblis Trigger was actually a half-truth: Sonic is indeed the Iblis Trigger, but his death would not stop Iblis's resurrection; in fact, his death would be the very event that would release Iblis from Elise's soul. The key to Iblis's freedom was an event that would cause Elise to become so consumed with despair or guilt that she would cry, and she had formed a very close (possibly even romantic) bond with Sonic.

Due to Sonic and Elise's actions in the past, Mephiles was erased from history.