The prologue is Sonic's last fight with Metal Sonic. With Dr. Eggman getting on in the years, his scheme in world domination has fallen into a doomsday plot that Sonic must stop.
Metal Sonic finally manages to outclass Sonic, so Sonic takes drastic action which leads to Metal Sonic falling into one of the jets of the Egg Carrier. This stunt prooves fatal as Sonic looses one of his legs. His friends stop Dr. Eggmans evil schemes. Turns out the reason Dr. Eggman has tried to destroy the world was because he given up tried to take over it. Dementia starting to set in as well as years and years of exposure from the Chaos Emeralds have caused him to become slightly insane, but found great satisfaction in seeing Sonic without his leg, seeing it as a victory enough to call it quits for good.
Some of Metal Sonic survived the wreckage, since the robot was made to endure great speed, his leg was grafted onto Sonic. However he was not as fast as before and Sonic claims it hurts when he runs. Over time his happy carefree attitude turned sour. He and Amy finally married, however Sonic's attitude worsen over time. Despite his pessimism and his cool sleek blue quills turning grey and dull, Amy stays with Sonic and cares for him even though she wonders if Sonic only married her because he had no reason to run anymore.
Eventually the cosmos remedies the absence of a blue speedster with a girl hedgehog who is coloured cyan. She pretty much takes the mantle as hero while heading back to Green Hill Zone, or Starlight City where Sonic and Amy live.
However a brand new antagonist to take up the role of conquer stands in her way and she was suprise when it was Sonic himself in his youth. Eventually she and Sonic discover it was actually Neo Metal Sonic, his conscious survived the destruction of his old body and laid dormant on the internet until he could reconstruct the upgrade that his former master gave him during Sonic Heroes. Thing is, even as Neo Metal Sonic, he takes the form of Sonic in his prime when he needs to match wits with the new hegehog while at the same time has a genious beyond Dr. eggman from his time on the internet, but also because he knows taking Sonic's younger form often will greatly mock the real older Sonic.
Oh, Tails is also head of his own company in advance technology and computer science and Knuckles who ages slower than his friends, has allowed a GUN base to be located where used to be Launch Base Zone and Rouge the Bat making Carnival Night Zone her home. Shadow looks exactly the same as before as he is immortal and perhaps teaches the new cyan hedgehog how to manipulate chaos energy.
All these just ideas.