Below the bedrock, the six (Jesse, Xara, Petra, Radar, Jack and Nurm/Lluna) make their way down a tower. Suddenly, a giant enderman appears and begins dismantaling the tower, but the group barely escapes and make their way toward the Oasis, a city that supposedly has an automated farm. At the Oasis, it is revealed that the city is in ruins. Xara gets angry over a destroyed bed, but eventually gets over it, and tells Jesse that the portal is the only way home, and that the secret weapon is in Fred's house at Fred's Keep. The group (Jesse, Petra, Radar, Jack and Nurm/Lluna) then go on a minecart track towards Fred's Keep.
On the way to Fred's Keep, the giant enderman takes out a portion of the track, causing the group to separate. Jesse and Jack are hanging on the edge of a cliff, and are cornered by people who "sniff out for outsiders" (one of whom is named PorkChop). They offer their assistance in exchange for their swords. Should the player give them their swords, PorkChop and company will assist Jesse and Jack onto solid ground before leaving. Likewise, should the player refuse the deal, Jack will fall towards certain death, and Jesse is able to climb up safely. Nonetheless, the group (Jesse, Petra, Radar, Nurm/Lluna and/or Jack) make it to Fred's Keep.
At Fred's Keep, the group meet with Binta, who informs the group that they can't enter Fred's house unless they win a trivia contest, in which Jesse accepts. Jesse is able to talk with other people at Fred's Keep in order to obtain more information about Fred, such as his favorite tool, or his pet chicken's name. Eventually, if Jesse wins the contest against the defending champion, Kent, he is able to search the house freely for the weapon. Likewise, if Jesse loses the contest, he sneaks into the house to find the weapon. It turns out, however, that the "weapon" is actually Fred's personal diary. Nonetheless, Jesse convinces that the people of Fred's Keep will have a much better life above the bedrock. Binta makes preparations while the group (Jesse, Petra, Radar, Nurm/Lluna and/or Jack) head towards Romeoburg.
On the way to Romeoburg, the minecarts hit a few ditches, and Petra, Radar and Lluna/Nurm and/or Jack are hit with potions of slowness from the guard that Romeo (disguised as Jesse) summoned. After an altercation, it is revealed that the guard is Ivor, and Ivor reveals that Romeo gave him the Order's amulet in order to find "the fraud" (the real Jesse). Jesse sets up Ivor with a cover story of the player's choosing to fool Romeo, and in exchange, Ivor allows Jesse to use the amulet. Ivor then disappears in a puff of smoke, and the group continue toward Romeoburg.
At Romeoburg, the group are confronted by members of Romeo's supposed "army", which turns out to be just a record player. Having caught them in their act, the two (Soup and Cal) let them in and let them take on Romeo's Death Challenge, which involves a bunch of hostile mobs infused with lava. The group are able to survive the challenge, and make it towards a cabin. Inside the cabin, Petra talks to Jesse abut not being able to talk to each other, but the two reconcile and put aside their differences. The two then solve a puzzle to find Romeo's "weapon", which is known as "#Potato451", and make it back toward the Oasis.
Back at the Oasis, Jesse sets off the firework to signal the people at Fred's Keep, and gives Fred's "weapon" to Xara. Suddenly, a giant enderman appears and begins demolishing the portal, but it is quickly rebuilt by Jesse. The player can then choose to leave Radar behind as a distraction for the enderman or bring Radar with him, and the group goes through the portal. Back in the Overworld, the group (Jesse, Petra, Jack, Nurm/Lluna and Radar/Binta, Cam and Kent) show up at the Order's old temple. Jesse notices a firework going off, and sees that Beacontown is under Romeo's control.
In a post-credits scene, Lukas meets with Romeo (disguised as Jesse), and asks him where the others are.