Jesse and his/her friends are forced to retreat to a safer area by horse, dodging the Wither Storm's attacks and building a bridge along the way. At a cavern, the group rest before they head off again. Gabriel/Petra's (whoever was trapped in the Wither Storm) memories begins to come back, remembering certain events from earlier episodes. Lukas may leave the group to search for his gang, while the wither sick Gabriel/Petra may be told by Jesse to stay behind to rest. Outside, Soren and Ivor are in an argument about the Wither Storm, but it is revealed that the Wither Storm was intentionally following Gabriel's amulet as Ivor had programmed, but failed to account for the amulet falling in Jesse's hands. Ivor apologizes for the trouble he caused, and says he has a solution to destroying the command block inside the Wither Storm. Accepting the idea, the group head off to Ivor's lab, located in the Far Lands. Axel and Magnus/Ellegaard take the amulet and split from the group.
The group decides to take a rest in a swamp and find some food before heading off again. Jesse and Ivor find a nearby witch hut with a cake adoring the window, but Ivor warns him/her that witches hate trespassers. Fending the cake, the witch arrives back at the hut, attacking Jesse with potions, but Ivor mysteriously disappears. Likewise, if you choose to return to the group with your findings (potatoes), the mobs still attack, but this time Ivor stays behind to distract them. Jesse and the group barely escape the onslaught and arrive at the Far Lands. They find an entrance that leads them to Ivor's lab, completing a maze and building a redstone contraption in the process.
Inside the lab, Jesse and Soren find the five treasures of the Order (prismarine shards, sea lantern, ghast tear, packed ice, and a dragon egg), and use them to open up yet another door, leading them to a room that appears to be designed after the Order of the Stone's battle with the Ender Dragon. As Soren explains the battle, Jesse opens the next door, containing the enchantment book and Ender Crystals, which Soren claims to have been destroyed during the battle with the Ender Dragon. Jesse realizes that Soren had lied about the story, and he admits that the command block was used to make the dragon vanish and the Order were never truly heroes, which ultimately caused Ivor to leave the group in the first place. Ivor returns and explains that he only intended to prove that the Order were false heroes using the Wither Storm. Jesse and his/her group of friends are in total shock about this ordeal, but quickly forget it as they have to defeat the Wither Storm. Ivor gives Jesse the enchantment book needed in order to break the command block, uses it on a diamond tool, and offers him/her a new set of armor. With everyone ready to go, they head back to the main land to fight the Wither Storm.
Back at Soren's temple, the group attempt to destroy the Wither Storm by provoking Endermen to be attracted to it. The Enderman are then able to remove blocks from the Wither Storm, creating a hole that allows Jesse to go inside the Storm. The group use all of the items that they have to create an invention that will allow Jesse to go inside the Storm. The invention works, launching Jesse and Reuben into the Wither Storm. Inside the Storm, Jesse and Reuben find the command block. With Jesse using the enchanted weapon, the command block begins to crack, provoking the Wither Storm, using tentacles to defend the command block. Jesse fends off numerous tentacles, and is able to crack the command block a second time, but the tentacles grab him/her and force him/her to drop his/her weapon. Reuben grabs the weapon and delivers it to Jesse, but is knocked into a pit. Jesse finishes off the command block once and for all, causing the Storm to explode.
Back on the ground, Jesse finds a gravely injured Reuben, who dies in his/her arms. A week later, back at Endercon, a memorial for Reuben is made and Gabriel and Petra have recovered. Gabriel may be told by Jesse to reveal that the Order of the Stone were frauds. Everyone congratulates Jesse and his/her group of friends, now known as the new Order of the Stone, for stopping the Wither Storm. The group then head off on their next adventure.