Story Mode is the standard mode of all Baldi's Basics games, with the exception of Baldi's Basics Plus and demo games.
The game begins with the player being asked by their friend to fetch the 7 notebooks for him at Baldi's Schoolhouse, since he would be late for the “eating practice” if he tried to get them by himself. Once they arrive at the school, they will be greeted by Baldi, who will later give them math questions each time they retrieve a notebook. Baldi gets angrier and angrier with each math question answered incorrectly, and he will begin chasing after the player. They have to keep on searching the rest of the notebooks while encountering other characters, and then try to reach the correct exit and escape the school.
The game begins with the player being greeted by Baldi, who will then give a brief instruction on how to play the game. The goal of the game is to retrieve all 7 notebooks scattered around the school. With each notebook taken, the You Can Think Pad will pop up on the screen along with math questions for the player to answer. At first, the questions can be easily answered, and picking all the correct answers results in Baldi giving the player a Quarter.
From the second notebook onwards, one of the three math questions will be made of illegible numbers and letters, making it impossible to answer.
Since the player has answered a question incorrectly, Baldi will start chasing after the player. With each notebook collected, his movement speed will increase. If Baldi manages to reach the player, the game will be over.
Since the player has already collected 2 notebooks, only 5 of them are left. Other in-game characters will also start appearing around the school, obstructing the player most of the time.
As soon as all 7 notebooks are retrieved, Baldi will inform the player through the school's intercom:
“Congratulations! You found all seven notebooks! Now all you need to do is... GETOUTWHILEYOUSTILLCAN! Hahahaaa!”
In this phase, the main objective is for the player to reach the exit and escape from the school before Baldi manages to catch up with them. There are four exits inside the school, but if the player tries to reach one of them, the door will turn into a wall at the last second, which displays a rough map of the school while showing your location. To win the game, they will need to activate all 3 exit routes before finally escaping with the last one. However, this is no easy task since Baldi's moving speed is extremely fast now, and Arts and Crafters will attack the player as soon as they see him. When that happens, he will teleport both Baldi and the player to the starting point of the game.