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 arrive at a portal which leads them to Boom Town, a place overrun by Griefers. Jesse, Axel and Reuben barely escape the onslaught by the griefers, arriving at Magnus' hideout. They talk to Magnus about leaving to go save the world, in which Magnus reluctantly agrees. Magnus 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 against Magnus with the prize of becoming the King of Boom Town. Jesse barely wins the Death Bowl, allowing Magnus to come along with them. The Wither Storm arrives and destroys Boom Town, forcing Jesse, Axel, Reuben and Magnus to retreat back to the temple through the Nether.
Likewise, if Jesse decides to find Ellegaard the Redstone Engineer in the previous episode, Jesse, Olivia and Reuben will return to the Nether and arrive at a portal which leads them to "Redstonia", which is labeled "the capital city of engineering". Jesse either crafts a Redstone Repeater or steals one from Disco Mickey's "cow disco" contraption, and re-enable the stair controls that were disabled by Calvin, leading them to the "Dome of Concentration" where Ellegaard is trying to make a Command Block. 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 here, 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, Gabriel or Petra (depending on who Jesse saved in Episode 1) greet them, and Jesse's friends attempt to find Soren the Architect, who supposedly has the Formidi-Bomb, something he claimed that would destroy anything. While trying to locate Soren using the Tracking Device, Ivor shows up on the map, shocking 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 should stop the Wither Storm, and they both go their seperate 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. 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 devouring the world, with the cost of their lives.