- "I promised him I'd save him, take him home, I promised him"
- — Thomas, talking to Teresa while mourning over Chuck's Death.
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 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 maze with stone walls. 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 hideous monsters called Grievers. 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 out of 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.
At night, just as the walls begin to close, Thomas sees Minho dragging Alby towards the Glade, because Alby has been stung by a Griever and is unable to run. Thomas wants to go and help, but the other Gladers tell him it is too late. Right before the walls close, Thomas steps into the Maze. Minho is angry at Thomas for not staying in the Glade, as he believes they will all die now. He leaves Alby by the walls and runs off. Then Thomas hears a Griever, so he drags Alby to the wall and starts tying him to the vines, working him higher and higher above the ground. Thomas lures the Griever away from Alby by running deeper into the Maze. 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 the wall vines. 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. In the Cliff, there is a Griever Hole, where things in the hole disappear.
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. Later, Thomas is elected Keeper of the Runners, taking Minho's place. When Thomas visits the girl, she speaks in his head. He learns that her name is Teresa. In time, Thomas discovers that Teresa triggered the End. No one knows 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 Tom develops a small feeling for her.
With the walls no longer closing, Grievers begin to take one kid each night.
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 bravely takes the hit by jumping in front of Thomas. Thomas feels guilty because he had promised Chuck to get him out of the Maze safely. Then a rescue team comes in and seemingly kill the WICKED member, 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. 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. In the end, about half of Group A and Group B make it to the safe haven, where they have to defeat new and even more hideous monsters before finally being transported to safety.
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, have not developed immunity 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 decides to receive his memory and leaves the group. They then formulate a plan to escape with the help of Brenda and Jorge. The group manages to escape, but are lead to believe that Teresa and the others have all escaped without them. Thomas and his posse escape to 'Denver', a city believed to be quarantined of The Flare. However, things turn out horribly and Newt joins his fellow Cranks (infected people). Later, after both groups led by Teresa and Thomas have shrunk considerably, they meet up again and join forces with Gally and a resistance group called the Right Arm. In an exploding final journey, Thomas leads an evacuation of over 500 Immunes from the WICKED compound just before it is blown up. He nearly dies, but Teresa throws herself in the way and is crushed under a concrete slab. 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, Brenda, and Minho. They emerge in 'paradise' and it is implied that they will repopulate the earth with their immune genes. In the end, Thomas kisses Brenda.
- He is immune amongst many others
- He was the creator of The Maze