The new Order of the Stone (consisting of Jesse, Axel, Petra, Olivia, but not Lukas) arrive at a temple in the jungle, eager to find treasure. After solving a puzzle, they go downstairs to find the treasure (an enchanted flint and steel), but are surrounded by hostile mobs. Barely escaping death, the Order decide to go see Ivor to talk to him about the flint and steel they found. On their way back, they are interrupted by the Blaze Rods (formerly the Ocelots and now without Lukas), talking smack about the Order as well as their former member, Lukas. After Jesse threatens to fight them, they stop annoying them and walk off into the jungle, Aiden warning Jesse that things won't always be this way.
Back at home, Ivor is found building a lava house that is deemed "unsafe" by fellow citizens. The player can either choose if it should be kept up or if it should be torn down by the citizens. Nonetheless, Ivor, Petra, Jesse and Lukas meet in the treasure room of the Order's palace. Ivor is shown the enchanted flint and steel when he realizes that it can lead them to the Eversource. Without time to waste, they all head back to the temple and find a portal, but as they light it, the Blaze Rods enter the portal first, followed by Jesse, Lukas, Petra, and Ivor.
The portal brings the four (Jesse, Lukas, Petra, and Ivor) to an island in the sky that is close to "Sky City", a city where unauthorized building is prohibited. Nonetheless, the four build over to Sky City by creating a bridge of dirt. From there, they meet up with Milo, a well-known person of Sky City. Before they could get information on the whereabouts of the Blaze Rods, the whole town is called for an emergency meeting. Isa, the founder of Sky City, threatens to arrest Jesse for building the bridge, but Ivor decides to turn himself in instead.
If the player goes with Ivor, Jesse and Lukas also turn themselves in and meet with the Founder. Jesse has a chat with the Founder, explaining why they aren't criminals. Nonetheless, the Founder sends all three to prison, but Reginald sees that they aren't actually criminals and are here to stop the Blaze Rods, so he lets them free to stop Aiden.
Likewise, if the player goes with Milo, Lukas will be captured anyway and Jesse and Petra go to a secret room in the inn that is home to the Build Club. It is also revealed that Milo is the leader of said club, but in order for the builders to be sure that they are "builders", Jesse has to craft either an anvil, an iron golem or iron boots. Milo, Jesse, and Petra then head to the palace to stop the Blaze Rods.
In the throne room, all five meet up and head to the resource room, lined-up with chests filled with spawn eggs. The group successfully finds the Eversource, which turns out to be a chicken who makes spawn eggs. Isa and Aiden both show up to stop them, with the Blaze Rods betraying Isa and pushing Jesse and Isa (Lukas as well if the player doesn't help him fight Aiden) off a ledge into the Void. Isa is surprised, however, that there is land below Sky City, and apologizes to Jesse for the issues prior. With that, Jesse and Isa build up to Sky City to stop Aiden (If Lukas was pushed off, he will have to stay to recover from his injury).
Back at Sky City, the Blaze Rods are spawning hundreds of mobs such as ghasts and zombies to destroy the city, but Jesse and Isa go through them with ease. Ivor gives Jesse a potion of the player's choosing to go past the other two members of the Blaze Rods to meet up with Aiden. Aiden spawns two Blazes to stop Jesse, but they are killed with ease. Aiden and Jesse then swordfight, with Jesse getting the upper hand and knocking away Aiden's sword. Realizing his fate, Aiden has no choice but to surrender and give back Jesse the enchanted flint and steel. Jesse can choose to send Aiden over the edge of Sky City, walk away from him, or take Aiden along (all choices but taking Aiden will lead to Aiden falling down a waterfall).
Back at the entrance to Sky City, the citizens have no choice but to fall down the waterfall toward land, surprised at what they see. Both Isa and Milo want to have full power of the people, but it is up to the player to decide if Milo should have power, Isa should have power, or if both should share power. Aiden and the Blaze Rods are formally arrested, while Isa gives Jesse the Eversource's crown as a token of gratitude. The four then head back home, but the portal instead leads them to an area filled with dozens upon dozens of different portals.