- "Heroes can come from unlikely beginnings... and broken frienships can lead to dark rivalries.
When the world is in danger, fate calls on the ordinary... to do extra-ordinary deeds... and go on journeys they had only dreamed of.
Our heroes, thrown together by fate... must now seek help from a legendary artisan of chaos/legendary inventor...
But the question remains... will it be enough to save the world?"
- —The narrator's intro. src
Note: The plot of the first three chapters of this episode can be entirely different depending on the player's decision in the previous episode of either going after Magnus the Rogue or Ellegaard the Redstone Engineer.
Chapter 1 (Boom Town)
- "I mean, sure, the world's in danger, but this is our chance to be heroes!"
- —Axel to Jesse in the Nether. (Determinant) src
In the previous episode, if Jesse decides to find Magnus the Rogue with Axel, Jesse, Axel, and Reuben (Pig) will return to the Nether and use the Nether Minecart System to get to Magnus. Axel wants to have fun even though he wanted everyone to keep moping in the previous episode, and Jesse tells Axel that they must reassemble the Order of the Stone immediately to stop the Wither Storm from destroying the world. On the way to Magnus, they are confronted by a Ghast, and Jesse can use either his/her sword, bow (determinant), or fishing rod (determinant) to defeat the monster. After defeating the ghast, the group arrives at a Nether Portal, which leads them to Boom Town, Magnus' kingdom of Griefers.
Chapter 2 (Boom Town)
- Axel: "Well, here you have it, Jesse. Boom Town in all its glory! What do you think? It's like I've finally come home. These are my people."
- Jesse: "Wow... Boom Town sure does keep you on your toes. Exciting stuff, huh?"
- Axel: "Yeah! Yeah! Now you're getting it!"
- —Jesse and Axel in Boom Town. (Determinant) src
Jesse, Axel, and Reuben arrive at Boom Town, a place overrun by griefers. Seeing the chaos of the place, Jesse uses the Amulet to locate Magnus and finds that he is in his hideout. However, a group of griefers surround the group and steals the Amulet from them. Jesse's Gang has a short fight with the griefers, sets off traps, survives TNT and Eggs, and retrieves the Amulet.
Chapter 3 (Boom Town)
Escaping the onslaught by the griefers, the group arrives at Magnus' hideout. Jesse's Gang meets Magnus, who traps them in a deathtrap of lava and TNT. The gang talks to Magnus about leaving to go save the world, which Magnus reluctantly agrees. Magnus reveals that the griefers of Boom Town "challenge the king for his crown." He tells them that he cannot leave the Tower because he is the King of Boom Town and that he could leave if Jesse beats him in the Death Bowl, where griefers face Magnus with the prize of becoming the King of Boom Town.
Jesse and Magnus arrive at the Death Bowl and start a challenge. Jesse can choose to go under the name of "The Amulet Holder," "The Ocelot Slayer," "The Destroyer," or "The Pig Master" if he/she decides to stay silent. Jesse builds a griefing tower with either wood, stone, or pink wool, which Reuben recommends using. He/she barely wins the Death Bowl, allowing Magnus to come along with them. Jesse delivers a victory speech, and the griefers start to challenge him/her because he/she is an easier target than Magnus. However, the Wither Storm arrives and destroys Boom Town, interrupting the griefers' challenge and forcing Jesse, Axel, Reuben and Magnus to retreat back to the Temple of the Order of the Stone through the Nether.
Chapter 1 (Redstonia)
- "Wow. Who would've thought that someday I'd really get to visit Redstonia? Ellegaard's Capital City of Engineering. Incredible. Do you think Ellegaard will be willing... you know, to help us?"
- —Olivia to Jesse in the Nether. (Determinant) src
If Jesse decides to find Ellegaard the Redstone Engineer in the previous episode, Jesse, Olivia, and Reuben will return to the Nether and use the Nether Minecart System to get to Ellegaard. Olivia admires the Redstone engineering behind the minecart system, and Jesse reminds her of the mission of reassembling the Order of the Stone and stopping the Wither Storm from destroying the world. A ghast attacks them on the way to Ellegaard, leaving Jesse with the options to defeat it with his/her sword, bow (determinant), or fishing rod (determinant). After defeating the ghast, the group arrives at a Nether Portal, which leads them to Redstonia, which is labeled "the capital city of engineering".
Chapter 2 (Redstonia)
After Jesse's Gang arrives at Redstonia, they see Ellegaard, who locks herself in her Dome of Concentration to try and make a Command Block. Ellegaard tells Calvin to disable the controls that can unlock the dome by taking away a Redstone Repeater. Jesse either crafts a Redstone Repeater by finding crafting materials around the place or steals one from Disco Mickey's Bovine Lava Disco contraption, and he/she re-enables the stair controls that were disabled by Calvin, leading the group to the Dome of Concentration.
Chapter 3 (Redstonia)
- "Your 'Witherstorm' problem was created by a Command Block, yes? That means a Command Block could be the perfect way of beating it!... Non-Goggle Guy/Girl, will you help me make one?"
- —Ellegaard to Jesse. (Determinant) src
Inside, they meet Ellegaard, who has attempted to create the Command Block for more than 6,451 times. She is surprised to see Jesse and Olivia and thinks Calvin sent them here. Jesse interrupts, saying that Gabriel the Warrior sent him there, and she remembers the Order before they split up. Jesse, Olivia, and Reuben can either agree to help her create a command block, or persuade her to come with them. Either decision will cause the Wither Storm to arrive and destroy Redstonia, forcing Jesse, Olivia, Reuben and Ellegaard to retreat back to the temple through the Nether.
Arriving back at the temple, Lukas greets them and reveals Gabriel or Petra (depending on who Jesse saved in Episode 1), who made it to the Temple. Gabriel/Petra reveals that the Wither Storm had destroyed everyone and everything back in their home, even Petra/Gabriel (the person who Jesse didn't save in Episode 1). When the group arrives at the room with the map, it is revealed that Magnus/Ellegaard (whoever who the player didn't choose to go after in Episode 1) has also been found and recruited and that Magnus and Ellegaard have a grudge against each other.
Jesse's friends attempt to find Soren the Architect, who supposedly has the Formidi-Bomb, something he claimed that would destroy anything. Soren is located on the map using the Tracking Device, which shows that he is in his fortress in the mountains. Ivor also shows up on the map, surprising Jesse's friends as well as the Order. They all agree to stop him before he arrives at Soren's Fortress. The player decides on whether to go to Soren's at night or in the morning, and they leave to go to Soren's Fortress.
At the fortress, Ellegaard and Magnus cause a ruckus regarding who would stop the Wither Storm, and they both go their separate ways. Jesse decides on whether to go with Ellegaard or Magnus, and Gabriel or Petra go along with Jesse to talk to him / her about a private manner. It is revealed that Gabriel or Petra got "Wither Sickness" from the Wither Storm, which is more fatal than getting it from a regular Wither effect. A creeper blows up behind them, causing the floor to give way to a library, where Jesse finds Ivor.
Gabriel or Petra show up to aid Jesse, and the three fight it out with swords and potions. Jesse's friends show up to stop him, but Ivor hits them with a splash Potion of Slowness, leaving them behind, and locks them up in the library by simply closing the door. Ivor then says that Ellegaard and Magnus will fail to stop the Wither Storm from devouring the world, with the cost of their lives.
- "In pursuit of answers, all our heroes found in Soren's Armory was deceit... and treachery.
Locked in a dark chamber deep in Soren's mountain, as the Order of the Stone rides off near certain doom, our heroes must ask themselves...
Would they find a way out of this dark tomb? Is there any way to cure Gabriel/Petra's Wither Sickness? Would they find a way to defeat the Witherstorm? Or will they remain, trapped, as it continues its ravenous rampage across the entire world?
Only time will tell..."
- —The epilogue of the episode. src
Depending on the choices made in previous episode, the plot may slightly differ. This list shows the narrative consequences.
- Whoever Jesse chose to go with at the end of "The Order of the Stone", Axel to get Magnus at Boom Town or Olivia to get Ellegaard at Redstonia, the following can happen:
- The entirety of chapters 1, 2 and 3 will be different depending on who Jesse chose to go with.
- When Jesse returns to the temple, Lukas will have fortified the entrance. The entrance will be fortified neatly if Jesse went to find Magnus, or will be fortified with random blocks if they went to find Ellegaard.
- Whichever Jesse went go find will either favour leaving the temple immediately or resting before travelling to Soren's fortress, vise-versa.
- If Jesse traded his/her sword with Otis, he/she will have a golden sword for the entirety of the episode. If Jesse did otherwise, then he/she will have a stone sword instead.
- Petra or Gabriel will appear depending on who Jesse saved in the previous one, one taking up a major role and will fight Ivor later on.
- If Petra was saved, and Jesse did not trade his/her sword with Otis, she will use a golden sword for the entirety of the episode. If Jesse did otherwise, Petra will have an iron sword instead.
- If Jesse did not create a bow in the previous episode, Lukas will hand Jesse a spare one as they are walking through the forest to Soren's fortress (strangely however, if Jesse supported the side to sleep before going to the fortress, Lukas will not give Jesse the bow but it still appears in their inventory and they can use it when fighting in the forest).