The introduction explains that The Order of the Stone is a legend of four heroes who once defeated the Ender Dragon. The game then returns to the present where Jesse (either male or female) is the protagonist. His friends Olivia and Axel are introduced, along with Jesse's pet pig Reuben. Axel brings the news of the Endercon where there will be a building competition with a chance for the winner to meet Gabriel, one of the heroes of The Order of the Stone.
The gameplay involves making choices that influence the story, as well as exploration and combat. The player must navigate through the environment, collect items, solve puzzles, and fight mobs. There are also sections where Jesse can create new items by arranging various items in a way according to a recipe. At the end of the episode an overview of the choices is shown, compared to those of players worldwide.