Yes and No.
If you are wondering if there is a Super Sonic final boss, then yes. Complete all three stories to unlock the last story, then get to the end of the last story. Super Sonic, Super Shadow, and Super Silver will fight Solaris (Mephiles and Iblis combined).
If you are wondering if you can get Super Sonic, Shadow, or Silver in the actual levels, then no (sadly). Ever since Sonic The Hedgehog 2, one had to collect all the Chaos Emeralds by beating special stages, and after that, one had to collect fifty rings in an actual level. In games like Sonic Adventure, Sonic Adventure 2, and Sonic '06, there are no special stages because the emeralds are used as plot devices in the story.
If you know how to use the Gems/Custom Actions, then you'll find this interesting. SEGA had planned to include a special "Rainbow Gem" in the store, which allowed Sonic to go Super. However, '06 is an incomplete game, and the Gem's coding is hidden away in the game's files. It can be accessed through complicated hacking, but all it does is run through a super sonic transformation animation (without any pretty colors of effects). It is completely useless.
If you want to try some hacking, many YouTube users have made hacks that allow you to play as an in-level Super Hedgehog. Just search "Super Sonic 06."
Hope this helps!
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no super sonic
super sonic
No, super Sonic is faster.
There is no dark super sonic!!!!!!! -_-
you cant sonic the hedgehog doesn't have super sonic