The game begins with an interviewer questioning William Afton, the creator of the

game's animatronic characters and the purple figure depicted in the previous
installments' minigames, on certain design choices he has made when building the
animatronics. Afton lists several features of Circus Baby, such as her ability to
make ice cream, inflate balloons at her fingertips, and take song requests and
dance to them. The interviewer is unsatisfied with this answer, as the features
Afton mentioned were not what he was referring to.

Sometime later, Afton's son Michael is a new employee of Circus Baby's

Entertainment and Rental, an underground facility and sister location to Freddy
Fazbear's Pizza, featuring animatronics that are rented out to children's birthday
parties.[1] These include new circus-themed variations of the original
animatronics: Funtime Freddy, Bon-Bon, and Funtime Foxy, as well as several new
characters such as Ballora, the Bidybabs, the Minireenas, and Circus Baby. These
animatronics originated from Circus Baby's Pizza World, which was made in response
to the popularity of Freddy Fazbear's Pizza, but had been shut down shortly before
it was supposed to open due to "gas leaks".[2] As his first night starts, the
assistant A.I. HandUnit assigns Michael his daily tasks. On Night 2, the power goes
out, and Michael must hide from the Bidybabs in order to reset the facility's
circuit breakers. Circus Baby, who turns out to be sentient, warns Michael to
ignore the instructions given by HandUnit to avoid being killed by Ballora, then
gives Michael her own instructions.

In between nights, dialogue shows Afton's daughter begging her father to allow her
to play with Circus Baby, which was initially created for her, but she was later
denied access to it by Afton for unknown reasons. In a post-death minigame, the
daughter manages to approach Circus Baby, but it extends a claw from its stomach
and pulls her inside, implying that the animatronic is now possessed by the girl's
soul.

On Night 3, Michael repairs Funtime Freddy, however, he is ambushed by Funtime Foxy

on the way back. He awakens the following night – Night 4 – in an animatronic suit,
having been kidnapped by Circus Baby and placed in the Scooping Room, which removes
the endoskeletons of the animatronics. After witnessing Ballora's endoskeleton
being taken out by the Scooper, Michael is left to survive the night against the
Minireenas before freeing himself. On Night 5, two technicians are found hanged,
and Michael is instructed by Circus Baby to destroy her emptied body by sending her
to the Scooping Room while evading an unknown animatronic following him.

If Michael brings Circus Baby's body to the Scooping Room, Circus Baby's voice
reveals herself to be Ennard, the animatronic following him. An amalgamation of
parts from the facility's animatronics, Ennard traps Michael in the room and uses
the Scooper to eviscerate and kill him; Ennard then disguises itself in Michael's
body to escape the facility. If the "Custom Night" is completed on the hardest
difficulty, an 8-bit cutscene shows Ennard abandoning Michael's decomposing body
after some time and fleeing into the sewers. Circus Baby says "You won't die"
repeatedly, prompting Michael to miraculously revive and stand up. Now hiding in
the shadows due to his disfigured appearance, Michael talks to his father about his
time in the facility and finding and freeing "her". He ponders his own survival
from being mutilated and used by Ennard, before declaring that he will find his
father. In the burned remains of Fazbear's Fright, Springtrap, which contains
Afton's body, emerges among the ruins.

Alternatively, Michael can disobey Circus Baby and retrieve a keycard, whereupon he
enters a private room where he has to fend off Ennard until 6:00 a.m. An easter egg
accessible in this area shows camera footage of the house featured in Five Nights
at Freddy's 4, implying that the house belonged to the Afton family and that the
boy depicted in its minigames was Afton's son and Michael's younger brother. After
finally completing his shift, Michael rests at home where Ennard has followed him.
The game refers to this ending as the "Fake Ending".