The following information may contain Spoilers. Please proceed at your own risk.
The Episode begins with Jesse, Petra, Lukas and Ivor going through several portals in the Portal Hallway, unsuccessfully trying to get back home. Petra tires of the repeated failures and argues with Jesse and suggests going into a Redstone portal, which they do.
The New Order of the Stone arrive in a Mesa Village, and are surprised to find that the Zombies there do not burn in the day and are much stronger. They discover a village named "Crown Mesa" nearby, but notice it has been abandoned. They meet a stranger named Harper, who tells them the Village's population has been neutralised by machine named "PAMA". The Order is soon captured by PAMA, and Lukas and Petra are chipped and are made "useful" by PAMA. However, Jesse and Ivor escape with assistance from Harper.
The group arrives at Harper's Secret Lab, where Jesse learns about PAMA's weakness to water, and that Harper is an old builder.
The trio are soon after tracked down by PAMA, and Jesse has the option to unchip either Lukas or Petra, the other being captured and taken along with Harper. Before being taken, Harper tells Jesse to find her headset.
Exploring Harper's Lab, Jesse, Ivor and Lukas/Petra discover a Mind Control Headset created by Harper, and Jesse uses it to control mobs chipped by PAMA to release Harper. Harper is again captured and the headset destroyed, but Jesse learns the location of PAMA's power source, a Redstone Heart which he/she must destroy to free PAMA before it gets Harper to build a portal to the Portal Hallway.
Jesse uses a Swiftness/Leaping/Invisibility Potion (The remaining ones from Sky City) to clear a path using TnT, and gets inside PAMA's base. Here, he/she attempts to disable 3 Redstone Spires while confronting mobs as well as Harper and Lukas/Petra. As he/she disables the final spire, PAMA attempts to hide its heart, but Jesse is successful in ripping it out despite efforts to sweet-talk Jesse from PAMA.
With PAMA defeated, Jesse goes with the others to the Portal Hallway and Harper reveals the existence of an "Atlas" which can help reveal the way the Order can go home. They use the Redstone heart as a power source, and one of the portals opens up into a very long stairway as the credits play.