The New Order of the Stone (consisting of Jesse, Axel, Petra, and Olivia) arrive at a temple in a jungle, eager to find a treasure Ivor told them about. After fighting off numerous hostile mobs in the jungle with style, the group enters the temple and is faced with a lava puzzle.
Jesse solves the puzzle, and the floor opens and reveals stairs leading to the temple's basement. The group heads downstairs to find the treasure. Jesse can find a cake, a pumpkin, and ultimately, an Enchanted Flint and Steel, drawing the group's attention. He/she tries out the enchanted treasure, and it illuminates the entire basement, revealing numberous hostile mobs surrounding them. Barely escaping with a "secret handshake" (The Warrior Whip, the Redstone Rap, the Griefer Grab, or the Building Bump) of the player's choice, the Order rushes up the stairs, only to be confronted by more hostile mobs and lava, which burns up the stairs.
The Order barely escapes the temple and decides to go see Ivor to talk to him about the enchanted flint and steel they found. On their way back, they are interrupted by former Ocelot members, Aiden, Maya, and Gill, who have forsaken Lukas and formed a new gang of adventurers, the Blaze Rods. They talk smack about the Order as well as their former member, Lukas. Aiden insults Jesse by saying that he/she takes all the treasures for him/herself and does not give anyone else a chance, and the Blaze Rods threaten the Order to give them the enchanted flint and steel. After Jesse threatens to fight them, they run off into the jungle.
- "That glow... that enchantment is the work of a very old group of builders, a group so old that they existed even before the Order of the Stone!... You see, if these builders truly existed, and if you found their temple... that means we're one step closer to finding... 'The Eversource!' What a beautiful sight!"
- —Ivor explaining about the Old Builders. src
Back at Beacontown, the Order is welcomed by adoring townspeople, including the Fangirl, who faints after Jesse high-fives her. 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 torn down by the citizens. Axel and Olivia will leave to help the citizens to either tear it down or to help cover up the lava with glass. Ivor will either complain about Jesse's rules or thank Jesse. Petra tells Ivor that the Order has found the enchanted flint and steel, and Ivor becomes excited and agrees to meet Jesse and Petra in the Order Hall.
Petra and Jesse meet Lukas in the Order Hall, and the group pays respect to Reuben (Pig), whose porkchop has been framed as a treasure. Lukas tells Jesse about how Aiden took over the Blaze Rods and is jealous of Jesse. As Jesse pulls out the enchanted flint and steel to show it to Ivor, the latter appears suddenly and scares the group. Ivor reveals that the enchantment on the flint and steel is made by the Old Builders, a group that existed even before The Old Order of the Stone, and the flint and steel can lead them to the Eversource, a treasure supposedly possessed by the Old Builders who built the temple. The Eversource is believed to be a "treasure or artifact that gives them an endless supply of materials."
Without time to waste, Jesse, Petra, Lukas, and the strangely excited Ivor head back to the temple and find a strange portal hidden in a chamber at the top of the temple that has to be lit by the enchanted flint and steel. As they light it, Jesse drops the flint and steel, and Aiden and the Blaze Rods appear, taking the flint and steel from him/her. The Blaze Rods enter the portal first, followed by Jesse, Lukas, Petra, and Ivor.
- "Please remain calm. Earlier today, outsiders built a bridge into our fair city from a distant island! Now, whether these outsiders know it or not, this is a violation of Sky City's most sacred law: no unauthorized building."
- —Isa to the Sky City Townspeople about the crime committed by Jesse's gang. src
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. They are confronted by a nervous citizen who tells them that unauthorized building is forbidden in Sky City. The citizen tells them that Aiden and the Blaze Rods went to an inn and runs off.
The group enters Sky City and sees how all building and crafting must be approved by "the Founder," who supposedly owns the Eversource and have built everything in Sky City. From there, they meet up with Milo, an infamous innkeeper of Sky City, who supposedly greeted the Blaze Rods. Milo is seen illegally trading sticks with another townsperson, and he tells the group that the Blaze Rods asked him where the Eversource is, to which he replied by saying that it is in the Sky City Palace with the Founder.
Before they could get information on the whereabouts of the Blaze Rods, the whole town is called for an emergency meeting. The Founder appears at her palace and threatens to arrest the four for illegally building the bridge, but Ivor decides that being arrested is the fastest way into the palace, where the Eversource is. He tries to turn himself in, and Milo tells Jesse that he has another way to get the group into the palace. The player can choose to either go with Ivor or escape with Petra and Milo.
- "I wouldn't be so sure of that, Jesse. This is MY world."
- —Aiden whispering to Jesse about his plan of taking over Sky City. (determinant) src
Helping Ivor: If the player goes with Ivor, Jesse and Lukas also turn themselves in and meet with the Founder. It is revealed that Aiden has won the Founder's trust and told her that Jesse's gang steals all the world's treasure for themselves and that they are planning to steal the Eversource.
Jesse has a short talk with the Founder, explaining why they aren't criminals. The Founder then invites him/her out for a private talk and shows him/her that nothing exists below them but Void and that all materials are extremely precious since if anything falls over the edge, it is gone forever. This is why she prohibited unauthorized building in order to prevent wasting of resources. She goes on to explain that the Eversource cannot simply give her endless materials, and she has to risk her life every day to retrieve the resources. Depending on how the player talks with her, the Founder can either believe that Jesse is not really trying to steal the Eversource or be convinced that Jesse's group is indeed a horde of dangerous criminals who wish to steal the treasure. Either way, the Founder imprisons them, for the fact remains that they illegally built a bridge into Sky City.
Reginald, the Captain of the Guards, puts the three in prison and confiscates their inventories. Jesse can convince Reginald that they aren't actually criminals and are here to stop the Blaze Rods. Reginald sees how they are more trustworthy than the Blaze Rods, and he lets them free with their inventories to stop Aiden. However, Ivor wishes to actually steal the Eversource, and Lukas states that stealing the Eversource is wrong, since the entire city depends on it. Jesse can choose to say that they need to steal the Eversource, that they should not steal it, or that they should just stop Aiden from stealing it.
- "I help you get into the palace, you help me steal the Eversource for my people. Unlimited resources for everyone!"
- —Milo to Jesse about his plan of liberating Sky City. (determinant) src
Leaving with Milo: Likewise, if the player goes with Milo, Jesse and Petra will escape from the guards and go to a secret room in the inn that is home to the Build Club. Milo asks Jesse to promise that he/she will not tell anyone about what he is hiding. It is revealed that Milo is the leader of the said illegal underground club.
Milo tells the two that he was once imprisoned by the Founder for "Egregious Wasting of Resources" because he dropped some dirt blocks over the edge. While he was in prison, he realized that just because building is risky doesn't mean that people should not learn to build at all.
The other members of Build Club are suspicious of Jesse's group, and in order for them to be sure that Jesse and Petra are "builders", Jesse has to craft either an anvil, a pair of boots, or build an Iron Golem to prove his/her abilities. It is revealed that Milo wishes to steal the Eversource for the people so that they can be free of the Founder's dictatorship. Milo knows that there is an unguarded window at the back of the palace that they can sneak in through, but it is far too high. Jesse crafts ladders to help reach the window, and Milo, Jesse, and Petra then head to the palace to steal the Eversource for the people.
- "So... the chicken lays the eggs, and the eggs... make monsters... and the loot from the monsters... made this place."
- —Jesse about the Eversource. src
In the throne room, all five meet up to find the supposed secret entrance to the Eversource. Jesse crafts a lever that opens a secret door, and all five arrive at the resource room, lined-up with chests, which are filled with spawn eggs.
The group successfully finds the Eversource, which turns out to be just a chicken who lays spawn eggs. It turns out that the Sky City's resources all come from the loot dropped by the monsters that are spawned by the spawn eggs laid by the chicken. Ivor wishes to steal the chicken, Lukas wishes to leave the chicken where it is, and Milo wishes to bring it to the people. Jesse can choose to support one of the three ideas, but the Founder and the Blaze Rods all show up immediately to stop them.
The Founder blames Jesse's gang for stealing the "one thing the city depends on to survive," and Aiden reveals his true natures to her. He spawns a creeper with a spawn egg, who blows a hole in the resource room. Lukas struggles to fight Aiden while the Founder dangles on the edge, struggling to pull herself up. Jesse can choose to save the Founder or help Lukas fight Aiden. Either way, Aiden will push Jesse and the Founder off the edge. Jesse and the Founder will fall into the Void, and if Jesse chose to save the Founder, Lukas will also fall with them.
However, it turns out that there is land below Sky City the whole time. Jesse and the Founder (and Lukas if the player chose to save the Founder) discover land and fall into a pool of water, and the Founder apologizes to Jesse for the issues prior. Nevertheless, numerous hostile mob fall from above, and it appears that the Blaze Rods are spawning monsters in Sky City. With that, Jesse and the Founder (alongside Lukas if the player decided) plan to 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. If the player chose to save the Founder, Lukas will stay behind. It is determinantly revealed here that the Founder's real name is Isa.
- "This was supposed to be my world, and you ruined it!"
- "Listen to yourself! That's insane!"
- —Aiden and Jesse. src
Back at Sky City, the Blaze Rods are spawning crowds of mobs such as ghasts, spiders and zombies to destroy the city. The Founder stays to protect her people from the monsters, and Jesse heads towards the palace to stop Aiden. Ivor offers 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 a creeper that blows Reginald aside upon seeing Jesse. He then spawns two blazes to stop Jesse, but they are killed off quickly. Aiden and Jesse then head into a 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 situation is getting out of control, and Jesse tells the townspeople to jump off the waterfalls. Although many do not believe that there is land below them, citizens have no choice but to follow him/her.
The citizens are extremely surprised to see that there is land below Sky City. However, The Founder and Milo have a disagreement; the Founder wants to reorganize the people while Milo wants everyone to run free. Jesse can choose to leave either one of them in charge or tell the to share power. Aiden and the Blaze Rods are formally arrested, while the Founder, whose name is ultimately revealed to be Isa, gives Jesse the Eversource Crown as a gift before heading off with her chicken friend, Benedict. Jesse sees several pigs and is reminded of Reuben.
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 to different dimensions.
- "That's... not what I was expecting."
- —Jesse's end quote. src