I didn't quite expect this boss battle coming. Dr. Eggman is in a scuba suit and causes all kinds of underwater trouble. He sets a blast to cause Sonic to have to flee or be crushed by the falling surroundings. I actually died twice trying to do avoid that.
The actual battle is pretty easy. You just have to wait for him to get close.
And warp him up alone. Takes a little awhile to get the trick but overall it's pretty easy.