Story Mode:Episode 2: Assembly Required
If the player decides to find Magnus, Jesse, Axel, and Reuben will return to the Nether and arrive at a portal that leads them to "Boom Town," a village 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, to which Magnus reluctantly agrees, but only if Jesse beats him in the Death Bowl, where griefers face 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 terrifying Wither Storm arrives and destroys Boom Town, forcing Jesse, Axel, Reuben, and Magnus to retreat back to the temple through the Nether.
Likewise, if the player decides to find Ellegaard, Jesse, Olivia, and Reuben will return to the Nether and arrive at a portal, which leads them to "Redstonia," labeled "the capital city of engineering." Jesse either crafts a repeater or steals one from Disco Mickey's contraption and re-enables the stair controls, leading them to Ellegaard's "Dome of Concentration." Inside, they meet Ellegaard, who has attempted to create a command block more than 6,451 times. She is surprised to see Jesse and Olivia and thinks Calvin sent them. Jesse interrupts, saying that Gabriel sent him here, and she remembers the Order before they split up. Jesse, Olivia, and Reuben agree to help her create a command block. On the third attempt, Ellegaard thinks the impossible command block is destabilizing, but the Wither Storm arrives and destroys Redstonia, forcing Jesse, Olivia, Reuben, and Ellegaard to retreat back to the temple through the Nether.
Arriving back at the safe temple, either Gabriel or Petra greets them, and Jesse's friends attempt to find Soren. 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 hideout. The player decides whether to go find Ivor at night or in the morning, and they leave to go to Soren's temple. At the temple, Ellegaard and Magnus cause a ruckus regarding who should stop the Wither Storm, and they both go their separate ways. Jesse decides whether to go with Ellegaard or Magnus, and either Gabriel or Petra goes along with Jesse to talk to him/her about a private matter. It is revealed that either 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. either Gabriel or Petra shows 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 so Ivor can kill Ellegaard and Magnus, as well as demolish the world.