Continuing from the events of FNaS 1, FNaS 2 features a brand new Sonic's Hero Pizza Palace location created in 2017. The clones from the previous location were taken and put in the back room. Instead, the restaurant chose to make the main stars robots rather than clones, as the clones had proven to be quite dangerous after Luigi's disappearance.
During the game, you play as Amy Rose, working the night shift from 12AM to 6AM for 5 nights, and then 3 nights overtime. During the week, you receive pre-recorded phone calls from Knuckles the Echidna, who has been hired as the night guard before you for this location. On your eighth night, you get jumpscared by Golden Sonic, leading to the full canon ending of the game where Amy dies.
The first of the minigames features real Sonic stepping into a cloning machine alongside Mario, Yoshi, and Tails, with the layout implying is the SHPP from FNaS 1.
The second minigame features Dr. Eggman going to the controls of the cloning machines and tampering with the cloning process. When the clone emerge, they have their black and red "evil" eyes, implying that Eggman was the cause of them turning evil at night.