After each battle, all characters, including those who may have been knocked out, are restored to full health. The player can also swap the current party with the reserve at any time. Once a turn is used, the player has to wait for some time until the next turn begins. The commands have different color tags and have different impacts, including healing the team (pink), providing status buffs (white), single-target attacks (orange), area attacks (red), poisonous attacks (green), and possible instant-kill attacks (black), among others. For each turn, the player is given choices for each character and must choose one of their three commands, which differ depending on the characters. The battles consist of turn-based random encounters, with several boss battles.
Upon defeating an enemy, the player will gain experience points and "Faz Tokens", which are used to buy upgrades such as "chips" and "bytes" to aid the player during the game.
Many enemy characters can be found throughout the game, each exclusive to their own area, which can be battled with. Initially, the world was depicted in a 2D Atari-like style, but as of Version 1.2 released in May 2016, the world has been redesigned into that of a pre-rendered 3D style. Once new areas are revealed and a special button is pressed in them, the player can use "jumping" to teleport between each area through an overworld map. The gameplay consists of exploring through the game world and accessing new areas. These tips frequently break the fourth wall due to Fredbear's seeming awareness of the situation he is placed in. Along the way, a character known as Fredbear will give the player tips on what to do next.
As the player continues, they collect more characters to place in their party, with there being 40 characters available in total from across the first four games. The starter characters, the original and toy versions of the first main games characters, can all be swapped in and out of the party. The player starts by choosing two parties consisting of four characters each. The game also has two difficulty levels to choose from, Normal and Hard. The seventh ending is Chipper's Revenge, where you fight one of Scott's older creations that he didn't finish.The player has two modes to play in: Adventure and Fixed Party. The sixth ending is played once the player collects the hidden clocks throughout the game. The same area also has a pond that the player can enter, which plays up the fifth ending. The fourth, played when the player enters the fourth layer of the Flipside, has the player encounter a figure who that they have entered the point of no return. The third is played when the player chooses Fredbear as party leader and bringing up a conversation with Fredbear. The second, played after defeating Scott in Hard Mode, has Scott accusing the player of killing the creator and declares that the game ends because no one is able to continue writing it. The first ending, acquired after defeating the owl guardian in Normal Mode, has Scott thanking the player for trying the game, albeit also mocking them for choosing the easiest difficulty. The game has multiple endings depending on the actions of the player. After each battle, all characters, including the knocked out ones, are restored to full health. Each character has a HP meter located at the top right corner by sustaining damages, the meter decreases until it reaches zero, which induces a KO (represented by a gravestone replacing the knocked out character) unless the player selects a resurrection command available on select characters. In battles, the player characters are on the right-hand side, while the enemies are on the left-hand side. Meanwhile, the battles against enemies, which are completely random, are conducted in a separate 3D playing field.