Mephiles' Appearances (In Order of Appearance)

Mephiles as seen from the assumed past (also the present-time structure based around the game); seen confronting Shadow.

Mephiles seen in the future ruined world with a corrupted-looking Chaos Emerald in front of the computer screen.
"Corrupted" is just a given name for it since there's no other explanation if whither or not he's consuming an emerald from a stolen timeline, or not, with altered colorings.

There is a Past Mephiles

• In Aquatic Base where Shadow is influenced to seal Mephiles back into the Scepter of Darkness, Shadow used Chaos Control, then he sealed him away. However, as you manage to defeat Mephiles Phase 2; in the end, the Scepter no longer works on him. 
  Well, here's why: Shadow used Chaos Control to halt him then continued to conceal him. Well, duh. Having sealed him now wouldn't have worked, unless you can support 'Chaos Control' again which Shadow does not perform, therefore leading to him in breaking out again from the Sceptor.
  

The Present Mephiles

• Knew only Shadow.
• Never seen to sought-out hatred for Sonic.
• Only fought Shadow.
• Never explained to Shadow (plot-hole) that he was wanting to fuse with Iblis to become Solaris. Shadow only took a guess in the Desert Ruins after learning about Mephiles in the past (at the end of Shadow's Story) where the boss battle; Mephiles Phase 2 begins. Mephiles should've explained his actions more deeply. He never did.
• Sure, he made clones of himself to trick Shadow into believing his.

Future Mephiles

• Knew only Silver & Blaze
• Blamed the world that the "Iblis Trigger" was what ruined the world as he shows Silver that his target is of course, Sonic The Hedgehog, who is in fact the Iblis Trigger.
• Also seen directing Silver & Blaze to the Terminal Station in helping their search for Sonic
• (Obviously can't be the same Mephiles chasing Shadow if the game matching all three of the character's stories were already being progressed and shown in the middle of the game).

Last Story Mephiles

Seen holding the corrupted Chaos Emerald. Cutscene is entitled as, "Mephiles' Smile,' as it is obvious that Mephiles has no mouth.

Blog Post Written & Constructed by: TheGothicEmperor7

In Conclusion

After brainstorming on this topic to list certain appearances that Mephiles has made in the game, they however are not well explained to carry-out in which order of appearance that they have appeared in each story from. As the gamer, you are assuming that it is the same Mephiles, but the challenging possibility rests among plenty of plot holes in knowledge that each Mephiles is 'not' one of the same and could be from various different time periods than the original because the space time continuum is constantly being changed as you played through the game, while the game is not clearly explaining the fabrics of time travel to you.

As it is known that Shadow 'does' release Mephiles from the Scepter of Darkness, unkowingly, after releasing him, Mephiles recalls events from the past that Shadow has no memory of the warps Shadow to the future while under the impression that he has been confined by him over a long period of time. This however could also be an effect that the events that when Shadow and Mephiles had met in Aquatic Base have not been written in history, yet. Therefore, with Mephiles only assuming traces of that memory could point that either it had been a paradox for him to assume that thought, or everything of this game was really devoted to Mephiles' knowledge of the future, not Silver the Hedgehog.

Sonic The Hedgehog '06 did contain plenty of beautiful graphics during its year in development but drastically withheld tons of disappointment in glitches and unexplained story plotholes, therefore rendering the game to looking rushed and incomplete. However, posing a unique Sonic villain (Mephiles The Dark) that actually has taken a swipe at Sonic's life, Mephiles The Dark I believe should be more recoginzed as an ongoing Sonic villain as he poses more to being more precise as a worthy Sonic villain than Dr. Eggman over the years in Sonic Gaming who is considerably destined to fail than compared to both Eggman and Metal Sonic.

And I also believe that this game needs a proper remake. One that can tell about time travel and paradoxes more thoroughly. The ending to this game was poor. Everything was erased led to all be for nothing. Like it NEVER HAPPENED.