The Game Jolt version upgraded the overworld's graphics to pre-rendered 3D. 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 player has two modes to play in: Adventure and Fixed Party.

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