This novel serves as a prequel to
The Maze Runner, chronicling the childhood and adolescence of Thomas and his friends inside WICKED (World In Catastrophe, Killzone Experiment Department), an organization devoted to curing the Flare, a brain-destroying virus unleashed after catastrophic solar flares scorched the Earth. The story reveals how the series' iconic maze was designed, built, and populated, and how Thomas came to wake up inside it with no memory of his past.
The novel opens from the perspective of a young boy later known as Newt, who lives in hiding with his parents and younger sister, Lizzy, sheltering from people driven insane by the Flare. Four strangers break in, kill both parents, and take both children, one man dismissing the boy as useful only as "a control subject" (6).
The narrative shifts to Stephen, a boy not yet five taken from his mother and brought to WICKED's facility. He refuses to accept his assigned name, Thomas, until a WICKED operative named Randall Spilker implants a pain-stimulating device in his throat and tortures him into compliance. Over two years, Thomas undergoes medical testing and classes while kept isolated. Around age seven, he meets Chancellor Kevin Anderson, who explains that WICKED studies the "killzone," their term for the brain where the Flare inflicts its damage, and tells Thomas he is among their highest-performing subjects. Dr. Ava Paige, the kindest adult Thomas has encountered, is then assigned as his personal doctor.
At roughly age eight, Thomas undergoes surgery to implant a brain-monitoring device. In the hospital hallway, Minho, another child receiving the same procedure, stumbles out screaming that WICKED is putting things in their heads. Inside the operating room, Thomas glimpses Newt, also recovering from the surgery, and spots Teresa, another WICKED subject, being dragged down the hall. Before Thomas is sedated, Teresa calls out: "Someday we'll be bigger" (45).
About a month later, a supervised meeting between Thomas and Teresa reveals a quick bond and a shared unsettling symptom: deep aches inside their skulls. Teresa whispers her belief that their implants are integrated with their consciousness. Officials then take Thomas and Teresa underground to a massive cavern where WICKED plans to build a maze. Two such mazes will serve as controlled environments to map immune subjects' brain activity toward a cure. Thomas, Teresa, and two other high-performing children, Aris and Rachel, are recruited to help design and build them.
Thomas discovers his door is unlocked, and Newt invites him and Teresa on nighttime explorations with Minho and Alby, another WICKED child who serves as an emerging leader. Newt leads them to a loft overlooking the Group B barracks, where the girls assigned to the second maze sleep, and points out his sister Lizzy, now renamed Sonya. He weeps, confiding that WICKED forbids him from acknowledging her, and Thomas promises to reunite them. On another night, the group is caught outside by Randall, who reveals Newt is not immune to the Flare. The others are taken to underground "Crank pits," tunnels where people in the advanced stages of the disease scream behind iron bars. A guard tells Thomas his nighttime gatherings will be banned for years.
Months later, Teresa discovers how to use their implants for telepathic communication, and Thomas masters the skill. Their mental connection becomes a constant lifeline. Teresa also learns to loop security camera footage, enabling the group to resume secret meetings. They befriend a younger boy renamed Charles, whom Thomas calls Chuck, and Chuck becomes a beloved member of their circle. Minho introduces Gally, another WICKED boy who claims to have arranged outside contacts, and the two announce plans to escape. The attempt fails: Randall forces Thomas to watch as a Griever, a biomechanical creature with deadly metal appendages, extends spinning blades toward a restrained Minho. Thomas begs Randall to stop, and the creature halts inches from Minho's face. Minho is emotionally shattered and withdraws from the group for over a year.
Thomas and Teresa spend months perfecting the maze's systems. Thomas fulfills his promise by sneaking Newt to the Group B barracks for a reunion with Sonya. At a high-level meeting, Anderson announces the Maze Trials have been shortened from five to two years because of a suspected Flare outbreak inside the complex.
On insertion morning, the boys assigned to Group A, the first maze cohort, line up for final exams. When Minho, Alby, Newt, and Gally realize Thomas and Teresa will not enter the maze with them, they erupt in anger, calling Thomas a WICKED collaborator. Thomas opens his mouth to plead, but something activates inside his brain, manipulating his thoughts and forcing him to say, "I'm sorry. There's nothing I can do" (188). The next day, he confirms WICKED has erased his friends' memories: They wander the Glade, the maze's central living area, as strangers.
Over the following months, Thomas watches via cameras as his friends build a community. One of the Glade's inhabitants, a boy named George, is stung by a Griever. The serum WICKED sends fails, and George attacks another boy before Alby kills him. Dr. Paige reveals WICKED engineered a mutated Flare that can affect immunes. Thomas later steals a research tablet and discovers Executive Order #13, a top-secret memo granting permission to release the Flare deliberately as a population-control measure. The virus mutated beyond expectations, becoming the catastrophe WICKED now fights to cure.
After Dr. Paige discovers that 19 staff members, including Anderson, are secretly infected, she declares a "Purge": The four immune teenagers must inject the infected with lethal syringes. Thomas personally kills the severely deteriorated Anderson. Dr. Paige assumes the role of chancellor.
Wracked with guilt, Thomas isolates himself for weeks before discovering footage of Newt climbing the maze wall and deliberately letting go in a suicide attempt that badly injures his leg. Dr. Paige sends Thomas to the Scorch, a devastated desert region, to test long-range monitoring. There, a young WICKED volunteer named Brenda reveals WICKED plans to send the Gladers, the maze's inhabitants, to the Scorch for further trials. On the return trip, Randall, now a full Crank, ambushes and kills Thomas's guards. Thomas kills Randall with his Launcher, an electroshock weapon.
Convinced WICKED will never find a cure, Thomas formulates a plan: He and Teresa will convince WICKED to insert them into the maze with their memories intact, then lead the Gladers to escape. Teresa persuades Dr. Paige to approve, and the two spend their last night making a pinky promise to see the plan through. On insertion day, Dr. Paige brings Thomas tea. As he drinks, she confesses she deliberately infected Anderson and his staff because they wanted to end the trials. Thomas realizes the tea is drugged. As he loses consciousness, Dr. Paige orders his Swipe, the memory-erasure procedure he fought to prevent. His memories dissolve until his mind goes blank, and Thomas opens his eyes in cold darkness: the opening moment of
The Maze Runner.
An epilogue of WICKED memos reveals the full betrayal. Chancellor Paige praises Teresa and Aris for their "loyalties to our purpose" (342), revealing both have been designated as knowing agents inside the mazes with their memories intact. A final memo from Teresa confirms she accepted this role, promising secrecy. She declares her belief in WICKED's mission and announces she will write three words on her arm before entering the Box, the elevator that delivers subjects into the maze: "WICKED is good."