- "Everything in the universe... starts out as just a block.
What comes of those blocks... is up to those who wield them. And in every block there lies the potential to create... or destroy.
Our friends have traveled far and wide... in search of the Order of the Stone. And a way to stop the Wither Storm for good.
But even well-laid plans can go awry... the strong can go weak... and beloved heroes can fall.
... the threat to this world -- to its very existence... is FAR from over."
- —The narrator's intro. src
Jesse finds Gabriel/Petra (whoever the player did not save in Episode 1) and finds out that they have amnesia and that the Wither Storm has split into three separate progenies. The group is forced to retreat to a safer area due the three Wither Storms' attacks. They escape by horse, dodging the Wither Storms and other hostile mobs along the way. They build a bridge along the way because the original bridge was destroyed by the Wither Storms. Before building the bridge, they discover that Endermen, who have escaped the End after Jesse flooding it, can slow the Wither Storms down due to their nature of moving blocks.
- "The world needs us, Reuben. So much of it has already been reduced to bedrock... and it's up to us to save the rest of it... Well, maybe that is a lot of pressure for just a person and a pig. But we have to find a way."
- —Jesse to Reuben outside the cave. (Determinant) src
At a cave, 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. They can talk about how they felt scared when they were in the original Wither Storm and claim that they have seen people wearing the Ocelot jacket that Lukas wears when they came out of the Wither Storm, thereby revealing that Lukas' gang, the Ocelots, may have survived.
Lukas is surprised by the news and tells Jesse that he wants to leave in search of the other Ocelots. Depending on how Jesse treated him in previous episodes, he may either admit that he is friends with Jesse or say that he did not have a great relationship with Jesse's gang. Jesse can either let him leave to find his friends, convince him to stay, or leave him on bad terms.
Magnus/Ellegaard (whoever Jesse didn't take the armor from) mourns over the death of Ellegaard/Magnus (who Jesse took the armor from), while Soren complains about how being emotional is getting them nowhere and goes outside for a moment to think.
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. Petra either shoos Reuben (Pig) off or tells Reuben that she needs to be alone. Reuben leaves the cave sadly, and Jesse goes out to talk to him, determinantly telling him that the group is cracking, that the Order of the Stone has failed, or that the world is depending on them.
Outside, Soren and Ivor are in an argument about the Wither Storms. It is revealed that the Wither Storms are intentionally following Gabriel's Amulet as Ivor had programmed, but he failed to account for the amulet falling in Jesse's hands. Ivor apologizes for the trouble he caused and says that he has a solution to destroying the Command Block inside the Wither Storms: using the Command Block Enchanting Book to enchant a weapon and destroy the Command Block with it while letting the Endermen dismantle the Wither Storms. Accepting the idea, the group head off to Ivor's laboratory, located in the Far Lands in order to get the Command Block Enchanting Book. 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 Storms at Soren's Fortress.
After a long journey, the group decides to take a rest in a swamp and find some food before heading off again. Jesse can find some potatoes in the swamp before discovering a nearby witch's hut with a cake adoring the window. Ivor warns him/her that Witches hate trespassers. Jesse is given to options to either go back and warn the group or sneak in the witch's hut and take the cake. If the player chooses to steal the cake, they can take the cake as well as a Potion of Leaping before the witch arrives back at the hut, attacking Jesse with potions, but Ivor mysteriously disappears. Likewise, if the player chooses to return to the group with their 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. Soren welcomes them to the edge of the world, and the group is immediately confronted by a Maze built by Ivor.
- "If the Order can't do this -- how are we supposed to? How are we supposed to do anything? We're nobody. The Order of the Nothing."
- "All I know is, the world is depending on us."
- —Jesse and Olivia at the Far Lands. (Determinant) src
Jesse can either choose to enter the maze or look for another way. Either way, zombies will appear, and the group is forced to retreat to the top of the maze wall. Jesse can use the Potion of Leaping to get to the top of the wall if he/she chose to enter the witch's hut. The group is split up, and Jesse has to navigate through the maze and fight witches and spiders. After the maze, Jesse, Olivia, and Reuben arrive at a platform and are faced with a gap between Ivor's Cottage and them, a Crafting Table, a Chest, and a Redstone structure. Olivia becomes pessimistic since Ellegaard discredited her ability of becoming a Redstone engineer and tells Jesse that they cannot manage anything. Jesse encourages her, and Olivia repairs the Redstone structure (a flying barge) with Jesse's help. The group rides to Ivor's Cottage in the flying barge, and it is determinantly revealed that Soren is afraid of flying.
The group find an entrance that leads them to Ivor's Cottage. Inside the cottage, Jesse finds some Redstone circuit near a lava curtain and needs a lever to activate it. He/she crafts a lever if he/she didn't already craft one in Episode 1. Jesse uses it to open a secret passageway, but it is closed before everyone could get in.
- "Why would you do that? You lied, even to your closest friends!"
- "All I can say is... I was a fool."
- —Jesse and Soren after Soren admitted the truth. (Determinant) src
Jesse, Soren, and Reuben, who got in the secret passageway, arrive at a secret room and find the five treasures of the Order of the Stone that Ivor has collected (Prismarine Shard, Sea Lantern, Ghast Tear, Packed Ice, and a Dragon Egg). With the help of Soren's stories, Jesse uses 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.
After Soren explains the battle, Jesse opens the next door with the help of his story and arrives at a room containing the Command Block Enchantment Book as well as the 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 the truth: the Command Block was used to zap the dragon out of existence, 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 who used the Command Block to falsify a legend.
Ivor arrives with the other members of Jesse's group, who have heard Soren admit the truth. Ivor 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 put it aside as they have to destroy the Command Block. 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 in memory of Magnus/Ellegaard (who he/she took the armor from) 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 Storms.
- "You're a hero, you know that? You just helped save the world!"
- —Jesse to the dying Reuben (Determinant). src
Back at Soren's Fortress, the group is greeted by Axel, who reveals that the Endermen are not angry enough. If Petra was saved, Gabriel will run off to fight the Wither Storm alone since Magnus/Ellegaard (whoever Jesse didn't take the armor from) did the same, and Ivor will run after him. The group heads inside to attempt provoke Endermen to be attracted to the Wither Storms. Soren gets scared and runs like a coward. If Gabriel was saved, Ivor will run after him. The Enderman are then able to remove blocks from the Wither Storms, 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. However, Axel/Petra is caught in a tractor beam, and it takes the whole group to pull them down. If Jesse let Lukas leave the cave, Lukas will return with the Ocelots and distract the Wither Storms with Firework Rockets. If Jesse convinced Lukas to stay, he will distract the Wither Storms with firework rockets alone. If Jesse left Lukas on bad terms, Lukas will not come.
The group builds the invention, which works, launching Jesse and Reuben into the main Wither Storm. Inside the Storm, Jesse and Reuben find Withered people and eventually the Command Block surrounded by the Wither Storm's tentacles. 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 with his/her weapon 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. 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. The group surrounds Reuben, and Jesse can comfort him as he struggles. Eventually, Reuben dies and turns into a porkchop, and the group mourns for him.
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. Jesse can give a speech about the adventure. Everyone congratulates Jesse and his/her group of friends, and Gabriel establishes them as the New Order of the Stone for defeating the Wither Storm. The group then head off on their next adventure.
- "And so it was that a New Order of the Stone was born. One whose adventures were only just beginning. For though the world had been saved, and the command block destroyed... there are many more worlds than just this one."
- —The epilogue of the episode. src
Depending on the choices made in previous episodes, the plot may slightly differ. This list shows the narrative consequences.
- Petra or Gabriel's roles will be switched depending on who Jesse saved in "The Order of the Stone", both leads to several differences.
- Gabriel saved:
- Magnus/Ellegaard will stay at the cave to keep Gabriel company as well as keeping him safe.
- Petra obtains her armor this episode and helps Jesse fight the Wither Storm.
- When Soren runs off, Ivor follows him to ensure his safety.
- Petra saved:
- Petra, incapacitated by the Wither Sickness, wishes to not stay in the cave when Axel and Olivia believe that she needs to rest. Jesse is left with a decision to support her to continue fighting, or tell her that she needs to rest. If Jesse supports Petra, she will go with Axel to distract the Wither Storm and will appear when Reuben dies. If told to stay in the cave, Petra is not seen again until the celebration at Beacontown.
- Magnus/Ellegaard will go with Axel to distract the Wither Storm. During which, Magnus/Ellegaard decides to leave Axel and recklessly fight the Wither Storm alone.
- Gabriel will run off when faced with the Wither Storm, which leads to Ivor following him to ensure his safety.
- Gabriel saved:
- When Lukas decides to leave off to find his friends and Jesse confronts him about it, depending on their relationship, Lukas will either do it out of not being happy around Jesse, or go out of respect to find his previous friends.
- If Lukas does leave, he will either arrive with the Ocelots during the Wither Storm fight to distract it with fireworks, or will not come back at all and will be last seen in the crowd during the celebration alone and clearly angry at Jesse.
- If Jesse remains silent when deciding which one will ride with (Petra or Gabriel), Lukas will decide himself that he will take Petra and Jesse will take Gabriel; however, this results in the opposite (He takes Gabriel, and Jesse takes Petra).
- Also, if Petra is the amnesiac, she and Gabriel will switch where they were standing when Lukas makes the decision.
- While the player is getting on the horses, they can see Magnus even if he died in Episode 3.