Alright. I wrote a story which I'm still writing on FanFiction.Net, but I've just finished Mephiles' mini-story within it. Since 'Sonic 06' never happened, I decided to write what I thought his backstory would be if he did exist still without the events of 'Sonic 06'. Here's my theory:
Mephiles was created in 1977 to be GUN's copy of the Ultimate Life Form (Shadow, who was considered to be too dangerous so was locked away on Prison Island). The machine he was created in malfunctioned, which caused some flaws within the project. His colours were different (his normal colour scheme when he's in his non-crystalline form), he couldn't blink and he had no mouth. His voice was also different, and he lacked in speed, except for his speed in attacks. Mephiles succeeded in his training, walking off elsewhere, having not spoken a word to anybody yet. One of the soldier's daughters decided to speak to him. Her name was Cynthia West and she was four years old. Mephiles realised that he had no name, so Cynthia decided to name him a unique name which she made up in her story. The name of one of the characters was Mephiles (who was revealed later to be the dark villain in the fairy tale Cynthia wrote). Mephiles easily got used to the name, and fell asleep his way on the lab floor that night, exausted, also not knowing how to count (discovering this when he had to play hide and seek with her). In 1983, a dark gloop was found by a lake. Cynthia was now ten years old and her father, Jeremy, had gone to stop some terrorists in Westopolis. Mephiles stated that the dark gloop was dark matter, knowing what it was because he was partially formed from it. However, this dark matter had much more strength and unstability than the one Mephiles was created from, and Mephiles' dark matter was quite unstable. Cynthia told Mephiles to warn the researchers, which he did. However, that night the dark matter escaped the capsule it was in through a crack, finding Mephiles and fusing with him. The next day Mephiles had almost totally forgot, feeling a little better about himself that day. Cynthia and Mephiles noticed that the dark matter had escaped, so began trying to find it. Mephiles was then hearing voices in his head, which was the dark matter speaking to him, using his mind. After giving up the search, three boys then started picking on Cynthia, named Dylan, Zak and Charlie. Mephiles asked them nicely to stop, but they carried on, so he used his dark powers to get them away from her. Both he and Cynthia were shocked. Not long after, Cynthia was told that her father was killed, not reacting at first. That night, though, she cried herself to sleep in Mephiles' new room. Three years after in 1986, Cynthia was still grieving, for she had no family left. When she went to get something to eat, Mephiles tried to think of a way to cheer Cynthia up, clicking his fingers when he came up with a solution. However, when he did this he accidentally teleported to the future, intensley watching what was happening (saying what was happening might confuse you if you haven't read the story). He then went back, being reminded by Cynthia that he only had one hour before going on his - finally - first major mission, which was stopping a chaotic riot. When he went, Cynthia gave him a wuick kiss, which of course made Mephiles embarrassed and caused a few soldiers to mock him. During the riot battle, Mephiles became outnumbered after defeating a good number of rioters. He used his dark powers against them, but was seen by some soldiers. They instantly knew he eas infected by the dark matter, so tried to knock him out or beat him until he was weak. For the first time Mephiles entered his Dark Form, fighting them off. He remained in shock afterwards, being taken back. He remembered that if he was seperated from the dark matter now, he would die. Cynthia had previously learned about this, and heard Mephiles' screams coming from the research lab, trying to get the researchers away from the controls so she could turn off the energy in the capsule. Her way failed, but Mephiles entered his crystalline form again to escape, teleporting away to Prison Island, where he encountered Shadow in his pod. Later Mephiles was found and locked away. A month later he was already weak, and Cynthia promised that she would do what she could to get him out. Mephiles, for once, showed emotion and cried, saying he couldn't take it. Cynthia tried to comfort him, and then left after a while. But Mephiles was in that cell for four years, barely being able to speak or lift his head. When he heard two guard-soldiers talking about Cynthia being trapped in a burning house in an attic, he tried to make them let him out, but they refused. The dark matter in his mind tried to tempt him to giving in a final time (one final time would be Mephiles' corruption). At first Mephiles refused, trying to escape on his own, but then gave in, knowing he had two minutes before he turned completely. He entered his crystalline form one final time, breaking loose, then using his powers to slowly kill the guards, then letting them go as he realised he had one minutes. So he teleported and grabbed Cynthia before she knew he was there, breaking out of the locked attic window (which had a hole in the floor near it, why Cynthia didn't go to it), shielding Cynthia's fall. Before Cynthia could speak to Mephiles the Hedgehog, she found herself speaking to Mephiles the Dark. Mephiles offered for her to join him on his quest for revenge, but she refused, thus making Mephiles angry. He then stated that she was just another human, and both the two battled each other. Cynthia scarred Mephiles' arm with her knife, and before Mephiles could kill her, GUN, the GUN Commander and a fire engine turned up. Mephiles then left. Cynthia became a commanding officer in GUN, and invented the Sceptre of Darkness to catch Mephiles in, also wanting to seperate Mephiles from the dark matter, despite if it could kill him. Ever since she and Mephiles were arch-enemies.