Okay, hear me out. My idea of how Sonic 4 should go down.

It picks up with GUN announcing a major shift after the debacle with Shadow, Eggman and the Eclipse Cannon and using a more advanced form of weapons made AI with drones similar to the GUN drones from the SA 2 game. As they do so, a new form of AI is being propagated to be sold to a growing number of customers (with Wade being the most opposed as he won't shut up about the Terminator and Matrix movies).

Sonic and Amy try to know each other but Sonic is too shy around her while Amy trains and shops with Maddie. Tom, Tails and Knuckles tries to encourage him to approach her to ask her out in different ways but they mostly fail (like the advice given to Tails to approach Zooey in Sonic Boom).

However, things go incredibly bad as GUN'S AI begins assimilating it's weapons programs while admitting it was plugging itself into other AI programs. When they ask what it is, Metal Sonic's eyes appear and it coldly says, "I am Sonic."

Soon the military officials are dragged to a new machine that roboticizes them in a rather cold and painful manner. Soon it spreads to the other humans turning them into bionic slaves including Tom and Maddie. This leaves only Team Sonic, Amy and (unfortunately) Wade as their only hope.

The AI Soon constructs a giant Metal Sonic dragon as it announces, "All Remaining Living Things, KNEEL BEFORE YOUR NEW MASTER!!!" Amy admits she's from a dimension where her Sonic turned into a robot to become more powerful to protect other people and animals but slowly went insane with power.

Team Sonic and Amy go Super to take him down which they do eventually only for Sonic to be attacked by Metal Sonic bodies that he battles even one going Super. Finally there is only one as they battle over a volcano like the Sonic OVA. Metal gets knocked down and slowly burning in the lava. Sonic tries to save him only for Metal to slap him away and giving a cold look as it willingly let's itself die.

Slowly everyone gets returned back to normal and Sonic and Amy agree to go on one date as they both admit having crushes on each other.

The after credits then cuts to one lone Metal Sonic happening upon an old temple depicting scenes of destruction and chaos. In the center pulsating with dark mist and flames is none other than the Scepter of Darkness from Sonic 06 as a familiar evil laugh emits from it.