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- "I just ... feel like I need to save everyone. To redeem myself."
- — Thomas to Newt, The Maze Runner
In The Kill Order, Thomas undergoes an operation for the Swipe so he can be sent into the Maze with the other Gladers. Through the entire operation, Teresa is by his side, scared about what will happen to her and Thomas, but calm, believing that WICKED will find a cure for the Flare for the sake of humanity. Thomas is then put into the Box and lifted into the Maze.
In the epilogue, it is revealed that Thomas was named after Thomas Edison because a WICKED agent pointed out a hanging light bulb in his mother's house, saying, "You know who made that, right? We should call this one Thomas."
In The Fever Code, Thomas is referred to as Stephen early on in the book. Two days have passed since Stephen has been taken from his family by WICKED, the same organization that wants Stephen to accept a new name: Thomas. However, Stephen continues to prove adamant until a man named Randall Spilker takes him to a chair, then injects a Pain Stimulator into Stephan’s neck, Stephen tries to stay with his old name, then at the touch of a button Randall activates the Stimulator, causing excruciating pain, seconds after the first wave of pain, Thomas wakes up, strapped with leather to the chair. Randall is in front of him with the button, Stephen starts to cry, and then Randall presses the button. This happens several times, after 4 waves of Pain, Stephen gets used to the torture’s never ending pain. Stephen tries to fake accepting his new name, Randall then responds saying “I don’t believe you.” and presses the button, causing more and more pain. Randall then continuously asks Stephen his name, giving up hope, he responds with ‘Thomas’ and accepts his new name. Randall administers a final wave of torture to remind Stephen (Now Thomas) that he can always inject a new Stimulator if he even mentions his old name. After this, Thomas does not see Randall for years, which he is thankful for, as he hated him.
Throughout the course of several years, Thomas spends much of his time attending advanced classes with different teachers. He meets and develops a fondness for Dr. Ava Paige, as she treats him with the most kindness out of all the WICKED staff members. Three years after the incident with Randall, he is allowed to meet a girl named Teresa, whose room was next to his. They form a close bond, and as they grew older, they were promoted to designing and building the Maze.
In The Maze Runner, Thomas wakes up in a lift with no memory except for his name. When the lift opens, he is surrounded by other boys who also have no memory except their names. This place is called the Glade. The Glade is surrounded by a gigantic Maze with the Walls moving and changing every single night. Every morning, the Doors to the Maze open, and every night they close. The Gladers do not want to be stuck in the Maze when the walls close, for they could be "stung" by the slug-like monsters called Grievers that lurk in the Maze. As Thomas adjusts to life in the Glade, he befriends a younger boy named Chuck.
When Thomas discovers that Runners go into the Maze to try to find a way out, he feels that he should be a Runner. Then, when a girl comes up in the Box, Alby and Newt call Thomas over because they feel that the girl and Thomas have a connection. Thomas denies having any memory of her, but he does feel like he knows her. The girl is in a coma and the Med-jacks take care of her.
In the morning, Alby and Minho go into the Maze to inspect an apparently dead Griever Minho found. At night, just as the walls begin to close, Thomas sees Minho dragging an unconscious Alby towards the Glade; the Griever had been playing dead and Alby had been stung. Thomas wants to go and help, and, ignoring the rules, dashes into the Maze right before the walls close. Minho is angry at Thomas for doing something so pointless, as he believes all three of them will die. At the sound of Grievers in the distance, Minho leaves Alby and Thomas and runs off, believing their chances will be better if they split up. Thomas drags Alby to the wall and starts tying him to the vines, working him higher and higher above the ground. When a Griever finally appears, Thomas lures it away from Alby by running deeper into the Maze. When he finds himself surrounded by several Grievers, he runs away, and then, turning around, he leaps over the one chasing him before it can slow its momentum.
He later meets up with Minho and the Grievers chase them. Minho tells Thomas to follow him and they go to the Cliff. The Grievers are still chasing them, but Minho has an idea based on what Thomas did with his run-and-jump maneuver. They both stand at the edge of the Cliff, and when the Grievers charge at them, they jump away and the Grievers fall over the edge. Several feet beyond the Cliff, there is an invisible hole seemingly suspended in mid-air, which is where the Grievers usually return after roaming the Maze.
In the morning, Thomas takes Alby off of the wall vines. Thomas, Alby, and Minho are the first people to survive in the Maze for a whole night. Alby is given an antidote for his Griever sting. When Thomas visits him, Alby tries to tell Thomas what he saw during his Changing. However, Alby grabs his own neck and starts choking himself. Thomas calls for Newt, and together they get Alby to stop hurting himself. Newt says that Alby is crazy, even though Alby says that he was being controlled and he didn't know what he was doing.
When Thomas visits the girl, she speaks in his head. Thomas is frightened and in denial about this at first. He learns that her name is Teresa. Teresa tells him telepathically that she triggered "the Ending." Thomas does not know what this means, but soon the walls do not close and bad things begin to happen.
When Teresa is fully recovered, she rushes to Thomas. They talk and begin to form a bond, with Thomas definitely having a crush on her. They also realize that they must have known each other before coming to the Maze.
With the Walls no longer closing, Grievers begin to enter the Glade each night, taking one kid at a time. Thomas and Teresa eventually figure out a code to the Maze. Thomas gets stung purposely by a Griever so he can remember his life before the Maze. He learns that there is only one way of escape: through the Griever Hole. The Gladers make it through the Griever Hole, losing half of their number, including Alby. They are greeted by someone who works for WICKED and Gally. Gally takes a knife and throws it at Thomas, but Chuck takes the hit by jumping in front of Thomas. Thomas is broken by this, going berserk and attacking Gally until he is pulled away by his friends. Then a rescue team comes in and seemingly kills the WICKED members, rescuing the Gladers.
In The Scorch Trials, Thomas and the other Gladers are rescued and brought to a safe dormitory, only to find out that it was all a hoax - they were never rescued and WICKED has been behind the whole thing. Teresa is taken and given to Group B, an all-girl experiment that has been run exactly the same as the Gladers (Group A). Phase 2 of the Trials begins as 'The Rat Man' (known as Janson in The Death Cure) from WICKED tells them they have two weeks to travel 100 miles of wasteland, in order to reach a safe haven and be given a cure for the Flare. On the way, the Gladers meet Brenda and Jorge, who say they are infected with the Flare and make a deal to reach the Safe Haven together.
Thomas's relationship with Teresa deteriorates drastically throughout the book, as Teresa is told by WICKED that unless she makes Thomas feel utterly betrayed (presumably to stimulate Killzone patterns in his brain), they'll kill him. Thomas does not believe her explanation, and there is a distinct coldness in his attitude towards her. Added to that is his budding relationship with Brenda, which seemingly makes Teresa somewhat jealous more than once.
In The Death Cure, Thomas awakes in a white enclosed room and is stuck in there for weeks until it is revealed to him that he and his friends will be able to get their memories back. The group is informed that some of their members, Newt included, are not immune to the Flare and are ultimately dying. Newt, Minho, Frypan, and Thomas refuse to regain their memories and are sent back to their rooms. Later, Frypan changes his mind, deciding to have his memories returned, and leaves the group.
Thomas and his friends then formulate a plan to escape with the help of Brenda and Jorge. Newt, realizing that his days are numbered due to the Flare, writes a note and gives it to Thomas, telling him only to read it when the time is right. The group manages to escape, finding along the way that Teresa and the others have all escaped without them. Thomas and his posse escape to Denver, a supposedly safe city that has not been badly affected by the Flare. However, things turn out horribly and Newt, being Flare-infected, is taken by some quarantine workers to the local Crank Palace (the place where infected people live out their remaining days). Thomas, Minho, Brenda, and Jorge try to get him out, but Newt refuses to go with them, aiming a Launcher at them until they finally leave in despair. Thomas reads the note Newt gave him earlier, finding that it reads, "Kill me. If you've ever been my friend, kill me."
Thomas and his friends then meet up with a group called the Right Arm, who are opposed to WICKED. The Right Arm has been kidnapping Immunes (Teresa and her group among them) as part of a ploy to take down WICKED. Thomas joins forces with them. A short time later, as he and a couple of Right Arm members are driving to where the Bergs are located, Thomas sees Newt among a group of Cranks on the road. He runs over to his friend, only to have Newt yell angrily at him because he did not follow the note's instructions. Newt then jumps him and pins him to the ground. Frightened by his friend's attack of madness, Thomas slowly reaches for his pistol out of self defense, only to have Newt notice and grab Thomas's hand, forcing the pistol to his own forehead. Newt yells at Thomas to kill him and make everything right, and Thomas, horrified but seeing no other choice, pulls the trigger.In an exploding final journey, Thomas leads an evacuation of hundreds of Immunes from the WICKED compound just as a series of bombs are being set off by the Right Arm. A concrete slab falls from the ceiling directly over him, but Teresa throws herself in the way and is crushed instead. Thomas says that he is very sorry, and Teresa says that she is, too. She tries to tell Thomas that she only ever cared about him, but she dies before she can finish her sentence. 200 of the Immune get out with Thomas, which include about half of Group A and Group B, before they make it to the Flat Trans that leads to a Safe Haven, which is apparently an island. They emerge in 'paradise', and it is implied that they will repopulate the earth with their immune genes. In the end, Brenda kisses Thomas as they watch the sunset together.
Thomas wakes up in a underground lift his memory and gets sent to The Glade a arena of teenager boys. Thomas meets Alby the leader of The Glade.
In a flashback Thomas is being dropped off by his mother and taken in by Ava Paige and WICKED Minho tells Thomas to wake up when they arrive Thomas grabs Chuck's replic they get send to a facility run by Janson
Physical Appearance and Personality
In The Maze Runner, Chuck told him he was around five foot nine and also described him (probably jokingly) as being as "ugly as fried liver on a stick". In The Kill Order, he is described as having sandy brown hair. In the movie, he is played by actor Dylan O'Brien, known for his role in the TV series Teen Wolf.
Thomas had always been an inquisitive person, before and after being sent to the Maze. He has a habit of becoming frustrated when answers are kept from him, something he experiences on a regular basis. In The Maze Runner, Thomas starts off as timid and somewhat aloof, but steadily grows more bold and sociable throughout the series.