- "It is said that within every loss, every challenge... and every failure... there is a gift.
When beloved friends/revered heroes [determinant] are lost... we find new ones in our heroes/friends [determinant].
When we're given grief... we find a way to give it back. / When faced with a mind-bending problem... we find a way to rise to the occasion. [determinant]
And when our band of unlikely adventurers are tasked with saving the world from the coming storm... they will bring together the bravest and the brightest to stop it.
But finding the last and most elusive member of the Order of the Stone and his legendary Formidi-Bomb... would prove their most perilous mission yet.
For some would rather our heroes' story end here... shutting the door on their adventurers forever.
But, like all doors, when one closes, another is bound to open..."
- —The narrator's intro. src
After Ivor locks Jesse and his/her friends in Soren's Fortress by simply closing the door, the slowness effect wears off, and Jesse and his/her friends have to think of another way to get to Soren and his Formidi-Bomb.
Jesse pulls out the Amulet, which shows that Ellegaard and Magnus are moving away. It is also revealed that the Wither Sickness of Gabriel or Petra (whoever the player chose to save in Episode 1) has gotten worse. Thinking quickly, Jesse uses the amulet and finds out that Soren is deep underground.
They dig a hole to a passage which leads them to an extremely large and heavily advanced Mob Grinder. A creeper blows up a portion of the tunnel, causing the amulet to slip out of Jesse's hands and fall onto a platform far from the passage. After fighting some hostile mobs, Jesse successfully retrieves the amulet, but slips on some water, causing him/her to fall towards death. Luckily, a creeper blows up the "crusher" just in time so Jesse and his/her friends fall down safely. From there, they are sucked in by gusts of water to the loot room, but more hostile mobs fall through to them because the "crusher" was blown up. Barely escaping, the group finds an End Portal and jumps in.
The group arrives at The End, and it seems that Lukas is crying, although he is actually trying to shield his eyes and avoid eye contact with Endermen. The group is confronted by several Endermen but manages to find Soren heading up a staircase. Jesse has the option to let Lukas lead the group or lead the group him/herself. The group decides that the only way to get to him is to safely walk past the Endermen, and they do so.
At the top of the staircase is a Wool World apparently built by Soren, but Lukas goes off in a rage, thinking this area was all there was. Jesse can talk with him and has the option to tell him Gabriel or Petra's secret of having Wither Sickness. Jesse finds and opens a secret puzzle door, which leads them to Soren's Laboratory.
- Olivia: "Okay, so if Soren is using those blueprints to teach the Endermen to build... And there's a disguise missing from the stand..."
- Jesse: "He must be conducting his experiment right now!"
- —Jesse and Olivia in Soren's house. src
Inside his laboratory, Jesse and Olivia stumble upon some music playing and a voice behind a door, thinking it is Soren. Opening it, it is revealed to be a jukebox playing a recording. Frustrated, Olivia searches around the room to look for some clues while Jesse listens to the rest of the records. One of the records talks about Soren making a suit to disguise himself as an Enderman, which Jesse later finds on his/her own. Jesse also finds some blueprints in a chest, in which Olivia believes that it is being used to teach the Endermen to build. After collecting the five clay bricks inside the room, Jesse goes outside to take the sixth brick from an Enderman, causing the Enderman to become "frustrated". Acting quickly, Jesse completes the crafting recipe, only to be knocked out by another person in an Enderman Suit.
Back inside, it is revealed that the person is indeed Soren. Soren feels suspicious at first, but immediately recognizes the Order when Jesse mentions the amulet. Agreeing to help Jesse with the Wither Storm problem, Soren gives a farewell song to his Endermen friends before the rest of the group enters the room. Gabriel or Petra and Soren happily meet/reunite, but their celebration is cut short as Endermen teleport into his house, forcing them to escape the End.
The group exit Soren's house but find that Endermen are everywhere in the End. With Soren's tips, Jesse breaks fountains to repel them with water. With the End flooded, the group leaves for the Overworld.
Back in the Overworld, the group are immediately welcomed by hostile mobs who broke free from the Mob Grinder. Jesse surprisingly finds that Soren did not really construct the Formidi-Bomb because the ingredients to create one are highly unstable and can explode when put near each other. Soren kills off the hostile mobs by summoning Iron Golems, and the group collects Gunpowder and the Super TNT, the ingredients of the Formidi-Bomb. Seeing that Endermen have teleported to the Overworld, the group uses a set of minecarts to escape them and head back up to the surface.
Upon arriving, Magnus and Ellegaard are there to assist the group with a crowd of hostile mobs, but the group finds that the mobs are running away from the Wither Storm. As the Wither Storm approaches, both Ellegaard and Magnus request Jesse to take their set of armor. Upon choosing either, Jesse makes haste to craft the Formidi-Bomb. Upon doing so, he/she throws it at the Wither Storm just before it explodes. After the explosion, the Wither Storm is presumed dead, but either Ellegaard or Magnus also die due to a blow from one of the Storm's tentacles, depending on whose armor that the player chose.
Jesse then helps out some survivors, but finds out that the Command Block of the Wither Storm wasn't destroyed, therefore allowing it to come back to life in three pieces that became three separate Wither Storms. Surprisingly, either Gabriel or Petra (whoever the player didn't save at the temple) shows up to assist them, but is forced to retreat to a safer area. It is also revealed that they have amnesia and have forgotten their names.
- "Faced with a devastating defeat... Our heroes will have to search deep within themselves... In order to rise above tragedy... Heal broken friendships... Untangle bitter rivalries... And find the strength to make one last stand against the storm."
- —The episode's epilogue. 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", one taking up a major role and the other appearing at the last minute.
- If Petra was saved, and Jesse did not trade his/her sword with Otis, she will use a golden sword for the entirety of the episode. If Jesse did otherwise, Petra will have an iron sword instead.
- If Jesse traded his/her sword with Otis, he/she will have a golden sword for the entirety of the episode. If Jesse did otherwise, then he/she will have a stone sword instead.
- Depending on the player’s past decisions that include Reuben, when Jesse gets sucked in by the command block, Reuben's reaction to this will differ.