Much like the first game, the player cannot leave the office but can track the animatronics' movements via a network of security cameras placed throughout the building. The office has three entrances (a hallway and two side air vents); in a departure from the previous game, none of these can be sealed off to prevent enemies from entering. Each vent is equipped with a light that can be used to check for any characters that are about to crawl into the office. Players are given a wearable Freddy Fazbear mask to ward off approaching animatronics; however, this strategy will not work on certain characters, who must be repelled by other means. A flashlight is also available, used to check the hallway and darkened areas of the camera feeds, as well as to reset Foxy via strobing. Unlike the previous title, the power supply for the cameras and vent lights is unlimited, but the flashlight has a limited battery life; if it runs out, the player becomes vulnerable to attack. In addition, a music box has been placed in one room and must be remotely wound up through the camera interface, to avoid being attacked by the Marionette, who appears when the music stops. Failure to defend oneself from the animatronics will result in a jumpscare, ending the game.
Unlike the first game, after the player is killed, there is a chance that, rather than the Game Over screen, one of four low-resolution minigames will appear with instructions given at the start of each. These minigames contain insight into the plot of the game.
The game consists of five levels referred to as "nights", increasing in difficulty. Completing all five adds one star to the title screen and unlocks an even more difficult sixth night, which in turn adds a second star and unlocks a "Custom Night" upon completion. In the Custom Night, the player can adjust the AI difficulty of the individual enemy characters (0 to 20) or play one of ten pre-set challenges. Completing Custom Night with every animatronic set to 20 results in adding the third and final star to the title screen.
Plot
The player character, whose name is later revealed to be Jeremy Fitzgerald, has started working as a night watch security guard at the improved Freddy Fazbear's Pizza. As he did in the previous game, a certain Freddy Fazbear's Pizza employee calls Jeremy on the phone in the office at the beginning of each night to explain both gameplay and parts of the backstory surrounding the restaurant. He explains that the new animatronics, which have special facial recognition software and access to a criminal database in order to protect the children from potential harm, were not programmed with a proper night mode; when things go silent, their programming tells them that they are in the wrong room and they seek out the nearest source of noise to find people to entertain, which happens to be the office.
As in the previous game, the animatronics' programming tells them that there should not be people in the restaurant after hours, so when they encounter Jeremy, they believe he is an animatronic endoskeleton without a costume and will attempt to stuff him into a spare Freddy Fazbear suit, killing him in the process. The employee explains that this restaurant has an unlimited power source at night, unlike the previous location, but there are no doors blocking access to the office, requiring the player to use a spare Freddy Fazbear head to trick the animatronics into thinking he is not an endoskeleton; he gives additional tips to help the player survive their shift. As more enemy characters appear as the game progresses, the employee informs Jeremy of their presence, their movement patterns, and some background information on their presence in the game. For example, he explains that the older animatronics are in the new restaurant, and have been retrofitted with the new technology, but as the company opted to redesign the characters, they are kept for spare parts.
As the game progresses, it is hinted that something is going on during the day, as the man on the phone mentions that rumors are going around and, later, that a police investigation is going on regarding the restaurant. Atari-styled minigames reveal that the restaurant has had a troubled past, as it was the location of a mass murder in which at least five children were murdered, with the culprit frequently appearing as a nameless purple figure (though later installments would give him the name William Afton). On the game's fifth night, Jeremy is informed by the employee that the restaurant has been put on lockdown due to an unspecified event, but which is in place to make sure no employees, present or former, can enter or leave. The man also mentions that the position of the restaurant's day shift security has a vacancy and Jeremy may be promoted to it, and that the owner of Fredbear's Family Diner (a restaurant preceding Freddy Fazbear's Pizza) will be contacted for more information on the incident. Notably, the check the player receives at the end of Night 5 is dated 1987, thereby establishing the game as a prequel to the original.
On the sixth night, the man on the phone informs Jeremy that the restaurant has been shut down for undisclosed reasons, although he mentions the use of a "spare yellow suit" and an issue of the animatronics not functioning properly. He also says that he will be taking over as night shift security guard when the restaurant reopens. If Jeremy is successful in surviving the sixth night, he is promoted to day shift to cover a birthday party the next day to make sure the animatronics do not cause any problems. A newspaper that is shown in the winning screen of the sixth night says that the restaurant will close down and the new animatronics will be scrapped; however, the older ones will be saved for when the restaurant reopens, hinting at the events of the first game.
