After the events of FNaS 4, the main 4 clones are sent to a storage unit. Their bodies are returned to normal and they are given help to prevent them from turning evil at night.
The game opens with a cutscene showing that the city is under attack, and because the original heroes are nowhere to be found, the clones take it upon themselves to deal with the threat. Tails develops a new weapon known as the Doppel-Buster, giving the clones a ranged attack, but at the cost of Sonic and Tails' ability to curl into a ball.
In the beginning of the game, the player travels to Peaceful Peaks to meet Dr. Golden, the villain of the game. There, they also see Toy Sonic and Toy Mario, now rebuilt with powerful weapons by Dr. Golden to be far more dangerous.
Throughout the story, the player travels across the many stages to defeat each of the toys. After defeating all 6, the player would then travel to 4 more stages to defeat the shadows, melty and unstable clones of the main cast.
Finally, after defeating the shadows, the player travels to the Golden Castle, Dr. Golden's home base, built over Angel Island. The player storms the castle, defeating many of Dr. Golden's mechs and the brand new Metal Sonic-styled mirrors to each of the clones. At the end, the player then uses the 7 Chaos Emeralds to defeat Dr. Golden and free him from the control of Eggman, ending the story.
In the other endings where the player does not get the Chaos Emeralds, the player instead defeats Dr. Golden, and his castle begins to crumble. The player would have limited time to escape and save the other clones. If any of the clones didn't make it out, it would lead to the bad ending. If the player saves all of them, it would lead to the neutral ending.