One of the portals leads the four (Jesse, Petra, Ivor and Lukas) to a Mesa biome. From there, Jesse and Petra find a supposed "super zombie" and kill it. After this occurs, several "super zombies" approach the group, indicating that Jesse, Lukas, Ivor, and Petra should follow them. The "super zombies" then lead the four to Crown Mesa, a town overrun by mindless people with red chips on the backs of their heads. Jesse then confronts Harper, who is believed to be behind all of this, but she escapes, and the four are brought by the townsfolk to see PAMA (Prototype Autonomous Management Agent), a supercomputer made of redstone equipment which mind-controls anything with the same chips as the townsfolk in their heads (which it describes as making them "useful").
PAMA welcomes the four to Crown Mesa but finds out that the four are not from there. It then asks them questions regarding how they got here and what their world is like, but it makes Petra and Lukas "useful" anyway. Just as Jesse is about to be made "useful", he/she and Ivor can either use an unsolvable math problem, a logic puzzle, or a riddle to make PAMA confused and to divert power. The two then escape alongside Harper to her secret lab. On the way to her secret lab, Jesse and Ivor find out that water destroys the chips used to control PAMA's henchmen. At the entrance, Jesse, Ivor and Harper are confronted by PAMA's henchmen, which includes Petra and Lukas. Jesse can unchip either Petra or Lukas by dowsing her or him with water. Harper gives Jesse a rose to give to "Harry" (an inanimate build with a zombie head and a jukebox voice) before she is abducted by whoever Jesse did not unchip.
At the secret lab, Jesse gives "Harry" a rose, removes ice from "Margaret"'s heart, and gives a redstone torch to another one of Harper's "friends". This allows Jesse to use a headset to control one of PAMA's henchmen, but to also migrate to another one if he/she gets surrounded. This is used to stop Harper from being made "useful". Harper then tells Jesse to head to PAMA's central core and to remove the Redstone Heart; shortly after, Harper is carried away by PAMA's henchmen. The three (Jesse, Petra/Lukas, and Ivor) then head towards PAMA's central core.
Inside the core, PAMA confronts Jesse with its henchmen, but they are killed with ease. Jesse then pours water on the redstone blocks connected to the heart in order to stop it. Just as Jesse is about to remove the Redstone Heart, he/she is confronted by Petra/Lukas (the person that the player left chipped earlier), but Jesse fights her/him off and is able to remove the Redstone Heart, effectively shutting down PAMA and freeing its henchmen from his control. The group then celebrates with the people of Crown Mesa before going back to the portal room.
In the portal room, Harper tells the four that she and some others made an atlas to chart routes between the portal worlds. She says that she doesn't have it, but knows someone who does, and reveals a flight of stairs.