The New Order of the Stone (consisting of Jesse, Axel, Petra, and Olivia) arrive at a temple in the jungle, eager to find a treasure Ivor told them about. 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 run off into the jungle.
Back at home, Ivor is found building a lava house that is deemed "unsafe" by fellow citizens. The player can choose if it should be kept up or if it should be torn down by the citizens. Axel and Olivia will help the citizens to either tear it down, or to help cover up the lava with glass. Nonetheless, Ivor, Petra, Jesse and Lukas meet in the Order Hall. Ivor is shown the enchanted flint and steel when he realizes that it can lead them to the Eversource, a treasure possessed by The Old Builders who built the temple which gives them endless materials. 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 that is close to Sky City, a city where unauthorized building and crafting are prohibited. Without knowing, the four build over to Sky City by creating a bridge of dirt. From there, they meet up with Milo, a well-known innkeeper of Sky City, who supposedly greeted the Blaze Rods. 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 the four for building the bridge, but Ivor decides to turn himself in instead. The player can choose to either go with Ivor or escape with Petra and Milo.
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. The Founder than invites him/her out for a talk to show him/her that nothing existed below them but Voic and that all materials are extremely precious, which is why she prohibited unauthorized building. Nonetheless, the Founder sends all three to prison, but Reginald, the Captain of the Guards, 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, 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 the said club, but in order for the builders to be sure that they are "builders", Jesse has to craft either an anvil or an iron golem. Milo, Jesse, and Petra then head to the palace to steal the Eversource for the people so that they can be free of the Founder.
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 Aiden pushing Jesse, Lukas (if the player decides) and Isa 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 (alongside Lukas if the player decides) build up to Sky City to stop Aiden. While collecting dirt for the tower they would build to get back up, Jesse discovers the other half of the Portal that brought him/her there.
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 (alongside Lukas if the player decides) go through them with ease. Ivor gives Jesse a potion of the player's choice 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. The player can choose to send Aiden over the edge of Sky City, walk away from him, or take Aiden with. If the player chooses to send Aiden over or walk away, Aiden will fall off Sky City in 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 Crown as a token of gratitude. The four then attempt to head back home using the portal Jesse found earlier on the land with Isa, but instead of leading them home, the portal leads them to The Portal Network, an area filled with dozens upon dozens of different Portals.