After the events of FNaS 4, Golden Sonic slowly melted to become Shadow Sonic. Using his supernatural abilities and mixing them with the power of the Time Stones from Little Planet, Shadow Sonic executed a plan to time travel back to 1991 to cause a time paradox. He travels to 2015, 2017, 2027 and 2028 to pick up each of the Golden Sonics from those time periods, as seen in the cutscenes prior to each night. He takes control of them and works with them to try and cause said paradox.

During the main story, you work as a newly hired night guard for Sonic's Fast Food Diner in 1991. During your week, you defend yourself against Origin Sonic, known as Golden Sonic by the staff. During your week, elements of the building begin to change, such as the vents in Cameras 5 and 8 being broken and needing to be manually sealed on Night 2, and a new vent being installed on Night 3.
At the end of the week, on the fifth night, Shadow Sonic appears to begin executing his plan. When the night guard comes back for the sixth night, the rest of the Golden Sonics appear, working to kill the guard.
At the end of the sixth night, at 6:01 AM, Origin Sonic gets into the office and attacks the guard, biting a little bit of his head off in an event that would later be known as the Bite of '91. Shortly after this, the building shut down, and the Golden Sonics were sent back to their own time periods once more.
Upon completing 6/30 mode, it is revealed that the night guard is Dr. Eggman.

From Night 7 onward, Dr. Eggman is in a coma. These nights are stress-induced nightmares. After Eggman awakes, he swears revenge on Sonic and vows to destroy the restaurant if it ever appears again.