- "We're stuck in a rut -- go through a portal, avoid dying long enough to get back to this stupid hallway..."
- —Petra's frustration. src
The episode begins with Jesse, Petra, Lukas and Ivor going through numerous portals in the Portal Network, unsuccessfully trying to find the portal to leads back to their home. After an adventure to a world full of fire and netherrack, the gang returns to the network, and Lukas catches on fire. Jesse can help him put off the fire or ignore it. It is shown that Lukas is constantly writing in a book, where he coins that world "Fire world."
Petra tires of the repeated failures and argues with the others, saying that they are not making any progress. Ivor wishes that those who built the Portal Network left some signs or guideposts. Petra becomes frustrated and suggests going through a Redstone portal, thinking that Redstone must mean smart people who will help them get home. She complains that Jesse has been leading the group every time and wants to leave on her own. Depending on the player's conversational choices, Jesse can either make nice with Petra or upset her, and Petra will either stay with the group or run off herself. Either way, Jesse, Lukas, and Ivor will also go through the portal and arrive in a mesa biome with no apparent sign of any Redstone.
- "They don't look happy."
- "They don't look anything."
- —Petra and Lukas about the citizens of Crown Mesa. src
After arriving in the mesa, Lukas continues to write in his book, which he claims to be "a book he picked up back in the White Pumpkin's place." The New Order of the Stone spots a road made out of sand on the ground, which is a sign of civilization. If Jesse made nice with Petra in the Network, Petra will rush forward to observe a strange zombie, and if Jesse angered Petra, he/she will find her observing the strange zombie herself. They surprisingly find that the zombies in this world do not burn in the day. After Petra attempts to fight the zombie, they discover that the zombie is much stronger, faster, and deadlier than a regular one and has a mysterious Redstone device on the back of its head, which also makes its eyes red. The zombie overpowers Petra, and the player can choose to help her or not.
Petra and Jesse (if the player chooses to help her) defeat the zombie, only to be confronted by a group of more red-eyed boosted zombies. The zombies do not attack them, however, and instead leads them to their village, Crown Mesa. Following the zombies, the four arrive at the village, and Ivor attempts to rip off the mysterious device on the back of the zombies' heads, only to find it irremovable. A sign nearby indicates that Crown Mesa holds a population of over a thousand people, but it appears strangely empty and seemingly abandoned. Chickens and zombies in the village all have the Redstone devices that make them stronger on the back of their heads.
They see a townsperson in the village, but the person keeps ignoring them. It turns out that he also has a mysterious device on the back of his head similar to the zombies. Jesse notices that there is no water in the wells. He/she suddenly sees a mysterious woman, who is the only person with no Redstone device on the back of their head, run into a house. The said person is surprised to see that the four do not have red eyes and tells them not to hurt any of the citizens of Crown Mesa. However, she immediately runs off after a group of townspeople enter the house and surround the four, telling them that they are not from the place and try to take them away. Jesse can either go with them or try to escape from them. Either way, the group will be captured.
- "I am making everything useful. Efficient. Effective. I am what you may call 'a computer' -- a thinking-machine. Designed to make things useful."
- —PAMA about itself. src
The Order is taken to PAMA (Prototype: Autonomous Management Agent), a computer who has been making everything in this world "useful," or efficient, by "chipping" and mind-controlling the world's population through Redstone chips, which are the mysterious devices they saw earlier. PAMA realizes that Jesse's group is not from its world. Jesse can choose to tell PAMA that they entered this world through a portal or not. Either way, PAMA will be interested in other worlds and plan to send its mind-controlled people through to other worlds and make all worlds "useful."
To retrieve more information about portals, PAMA threatens to install Redstone chips into Lukas and Petra and make them "useful;" however, it promises to delay it if Jesse can tell it how to enter other worlds. Jesse can tell PAMA that he/she doesn't know or refuse to cooperate with it. Either way, PAMA decides to get more information and makes Lukas and Petra "useful." It also tries to make Jesse and Ivor "useful," but Jesse confuses PAMA by telling it a paradox, a self-contradictory statement. The computer glitches while trying to process it, giving Jesse and Ivor time to escape. The mysterious person from before shows up, and it is revealed that she is the creator of PAMA. Jesse and Ivor escape from PAMA's mind-controlled puppets with assistance from her.
The stranger leads the two away and distracts the mind-controlled monsters, buying them time to get to her secret lab. After jumping into a cave, Jesse and Ivor discover that PAMA's mind-control chips can be deactivated with water, which means that they can free Petra and Lukas by pushing them into water.
- "Jesse -- you and your friends -- you're our only hope!"
- —Harper to Jesse before her capture. src
Jesse and Ivor head to the secret lab, while Ivor deems the woman "intriguing" and shows a little interest in her. The mysterious woman suddenly shows up, much to Ivor's surprise. She introduces herself as Harper and tells the two that she designed PAMA to automate things, but it went out of control and started making everything "useful." It is revealed that Harper is an Old Builder and has helped build the Portal Network. However, she destroyed the exit portal back to the Network in her world so that PAMA cannot expand into other worlds. That is why PAMA is interested in catching Harper, because she knows how to build an exit portal.
The group arrives at the secret lab, where Harper uses buckets of water to defend them from PAMA's forces. However, the trio is tracked down by PAMA before she can finish. Mind-controlled Petra, Lukas, and several spiders break into the lab, attacking them. Jesse has to option to un-chip either Lukas or Petra by pushing them into the water. Before he/she can un-chip the other, however, the still-chipped person captures Harper and leaves. Before being taken, Harper tells Jesse to find her Mind-Control Headset.
Exploring Harper's lab, Jesse, Ivor, and Lukas/Petra (whoever the player chose to save) find TNT in a chest and discover the Mind-Control Headset created by Harper, and Jesse uses it to remotely control mobs chipped by PAMA to get to Harper. Jesse tries to save Harper through the controlled mob, but Harper is captured again by more mind-controlled townspeople. Before being captured, Harper tells Jesse the location of PAMA's power source, the Redstone Heart, which he/she must remove in order to shut down the computer before it gains access to other worlds. Harper states that Jesse and his/her friends are their only hope, and PAMA's forces locate the headset. PAMA starts trying to make Jesse's headset "useful," and Jesse pulls it off before it explodes. Knowing that Harper put all her trust in them, Jesse, Ivor, and Lukas/Petra take buckets of water and head out to destroy PAMA before it takes over all other worlds.
- "Let's go wreck the heck out of PAMA."
- —Jesse src
Jesse's gang find the entrance to PAMA's Control Core, where the Redstone Heart is located. However, many mind-controlled mobs are patrolling nearby, and Jesse has to clear a path using the TNT he/she found in Harper's secret laboratory. Jesse uses a Swiftness/Leaping/Invisibility Potion (One of Ivor's two remaining potions after the Sky City adventure) to clear a path and finds that PAMA's chipped forces have started to build an exit portal already. Figuring he/she must deactivate PAMA immediately, Jesse enters PAMA's Core.
In the Control Core, PAMA senses Jesse's presence and starts taunting him/her, telling Jesse that his/her plan to deactivate it is futile. Jesse finds three Redstone Spires that power the Redstone Heart and disable them by pouring water to wash away the Redstone. PAMA deploys mind-controlled zombies and spiders to stop him/her; although they are strengthened by the mind-control chips, Jesse is able to fend them off by knocking them over the edge of the Control Core's platform. After disabling the first two Spires, PAMA sends a mind-controlled Harper to confront Jesse and attempts to trick him/her into using his/her final water bucket on Harper. Having only one water bucket left, Jesse cannot use it on Harper while there is still on Redstone Spire left. He/she disables the final Spire by pouring water and later frees Harper by pushing her into the same water.
Knowing that its Heart is now vulnerable, PAMA tries to hide/protect the Redstone Heart while sending mind-controlled Petra/Lukas (who the player didn't save) after Jesse. Petra/Lukas try to damage Jesse's morale by reminding him/her of Reuben (Pig) and how he/she has failed to lead the gang home. However, Jesse is successful in reaching the Heart. Using Petra/Lukas to punch Jesse, PAMA forces Jesse to dangle off his/her friend. It attempts to destroy them both, but it has underestimated Petra/Lukas' willpowers. Petra/Lukas resists and gives Jesse the time to rip the heart out. As a final struggle, PAMA tries to sweet-talk Jesse and convince him/her to save it. If the player chooses to help it, PAMA will use Petra/Lukas to knock Jesse over the edge and kill him/her. This results in a game over. If the player insists to rip the heart out, Jesse successfully removes the Redstone Heart and deactivates PAMA.
- "Now when we built this place, we also made something that sorta acts like a compass/map/navigator. We called it 'The Atlas'... In order to find the Atlas, we need to track down the rest of the Old Builders (Still don't like that name.)"
- —Harper to Jesse's gang. src
With PAMA defeated, Jesse's gang, along with Harper, return to Crown Mesa. The townspeople, however, despise Harper for creating PAMA. Jesse can choose to either defend Harper and convince the townspeople that she would help them with reconstruction of the mess PAMA left or choose not to defend Harper, leaving her forever remembered as a "mad scientist."
The group lights the exit portal PAMA built and return to the Portal Network. Harper reveals the existence of a Portal Atlas, which the Old Builders have designed to help navigate the Portal Network and reveal the way the Order can go home. It turns out that she does not have this Atlas, but she knows where to find the rest of the Old Builders and ask them for the Atlas. They use the Redstone heart as a power source, and one of the portals opens up into a very long stairway leading to the Old Builders' Atlas and their way home.
- —Ivor's end quote. src