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This page documents the events that take place in the second episode of Minecraft: Story Mode. 
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If the player decides to find Magnus, Jesse, Axel and Reuben will return to the Nether and arrive at a portal which 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, in which Magnus reluctantly agrees, but only 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 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", which is labeled "the capital city of engineering". Jesse either crafts a repeater or steals one from Disco Mickey's contraption, and re-enable the stair controls, leading them to Ellegaard's "Dome of Concentration". Inside, they meet Ellegaard, who has attempted to create a 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 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 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 temple, Gabriel or Petra greet 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 on whether to go to 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 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, so Ivor can kill Ellegaard and Magnus, as well as demolish the world of Minecraft.