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 because the original bridge was destroyed by the Wither Storm. Before building the bridge, they discovered that Endermen can slow the Wither Storm down due to their nature of moving blocks. At a cavern, the group rest before they head off again. Gabriel/Petra's (whoever was trapped in the Wither Storm) memories begin to come back, remembering certain events from earlier episodes. Lukas may leave the group to search for his gang, the Ocelots, while the Wither Sickness is taking over Gabriel/Petra (Whoever Jesse saved in Gabriel's Temple), they 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: using the Command Block Enchanting Book to enchant a weapon and destroy the Command Block with it while letting the Endermen dismantle the Wither Storm. Accepting the idea, the group head off to Ivor's laboratory, located in the Far Lands. Meanwhile, Axel and Magnus/Ellegaard (whoever Jesse didn't take the armor from) take the amulet and split from the group to keep the Wither Storm at Soren's Fortress.
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's 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) and warn them about the witch, 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 Cottage, completing a maze and building a redstone contraption in the process.
Inside the cottage, Jesse uses a lever to open a secret passageway, but it is closed before everyone could get in. Jesse and Soren, who got in the secret passageway, 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. Soren tells Jesse how he destroyed all the Ender Crystals and Gabriel poked the dragon dead with a sword. 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 Soren 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 because he didn't want to be in a group of "cowards." Ivor returns with the other members of Jesse's group and explains that he only intended to prove that the Order were false heroes using the Wither Storm, only to lose control of it. 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, lets Jesse use it on a diamond tool, and offers him/her a new set of armor. Jesse can choose to keep the armor he/she is already wearing or take a new set of armor. Either way, Ivor suggests that Jesse can also take some armors for his/her friends. With everyone ready to go, they head back to Soren's Fortress to fight the Wither Storm.
Back at Soren's Fortress, 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. Jesse can choose to create a TNT launcher, a rocket minecart, a flying machine, or (if he/she snuck in the witch's hut) use a Potion of Leaping and if he/she stays silent, either Olivia or Petra will suggest that they create a Reuben launcher. 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 out of the Wither Storm, where he fell to his unfortunate death. 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 and turns into a porkchop. A week later, back at Beacontown, a memorial for Reuben is made and Gabriel and Petra have recovered from their Wither Sickness and amnesia. Gabriel may be told by Jesse to reveal that the Order of the Stone were frauds, or keep the secret that almost everyone used to believe in. 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.