At some point after Newt arrived in the Glade, he and Alby formed the Gladers after discovering that the box elevator delivered a new boy to the Glade every 30 days. Two years later, Newt witnessed the arrival of a teenage boy named Thomas and taught him about the Gladers and the Maze that surrounded the Glade. The next morning, Newt woke Thomas up early and showed him a Griever, a violent, slug-like cyborg species that constantly attacked the Gladers. Shortly afterwards, Newt was informed by a younger Glader named Chuck that the box elevator had delivered a girl to the Glade. After Alby and Newt pulled the unnamed girl out of the box, the girl awoke and questioned her surroundings before she fell into a deep coma. The girl was then taken into the care of the med-jacks. That night, a deranged Glader named Ben attempted to kill Thomas, but was hit with an arrow by Alby and banished to an area in the Maze called the Cliff and Newt was tasked by Alby to inform Thomas of Ben's banishment, which he did. A few days later, Newt, Alby, Thomas, and Chuck awaited the return of a Glader named Minho, who reported that he noticed a dead Griever. Alby, though reluctant at first, ventured into the Maze with Minho to look for the deceased Griever. When they didn't return to the Glade as the sun started to set, Thomas grew worried and awaited their return with Newt. Minho eventually returned with Alby seriously injured, as he was stung by the Griever, but was rescued by Minho. Before Minho could turn Alby over to the med-jacks, however, the stone doors leading to the Maze closed, separating Newt from Thomas, Minho, and Alby. The next morning Newt found and recovered Alby's body in the Maze and injected him with a serum to treat his wounds and interrogated Thomas and Minho, who were attacked by Grievers that same night. Minho got into an explosive arguement with a Glader named Gally sometime later and Gally ran off into the Maze and went missing. After Gally's disappearance, Newt assigned Minho to train Thomas to become a Runner, a Glader who runs around the Maze and maps out changes in the Maze after discovering that Thomas had a telepathic link to the comatose girl, Teresa. After a few days of training, Minho and Thomas returned to the Glade one evening to report their discovery to Newt and Alby: The Cliff contained a locked tunnel for people to escape the Maze and is possibly the place where the Grievers originated. Before Newt and Alby could question them further, however, Chuck informed them that Teresa was awake, and Newt and Alby found Teresa in the midst of a conversation with Thomas. Alby ordered Newt and a few other Gladers to imprison Teresa in the slammer, a jail cell in the Glade, though Thomas later persuaded Newt and Alby to release her. Later, Gally returned to the Glade and warned the Gladers that the Maze's creators will kill them, before he was attacked and dragged away by a Griever. After Teresa's release, Teresa went with Newt to map out changes while using her telepathic link to contact Thomas, who was with Minho. While in the Maze, Thomas was attacked and stung by the Grievers, but was rescued by Minho and injected with the serum. Later, Newt and the other Gladers noticed that the stone doors leading to the Maze stopped closing at night and the Gladers imprisoned Thomas in the slammer to keep him safe from the Grievers. Thomas awoke two days later and had Newt call a gathering to reveal his plan to escape the Maze. Newt was present at the gathering where Thomas revealed that the Maze was created by an organization called WICKED and also abducted the Gladers. Thomas also revealed that WICKED forced he and Teresa to design the Maze and that the letters on the Gladers's maps spell a code that must be typed into a computer near the Cliff to unlock an exit from the Maze and deactivate the Grievers. Shortly after the gathering, Thomas led the Gladers through the Maze, but they were attacked by the Grievers. Alby chose to sacrifice himself and Newt tried to rescue him, but he was too late, and Alby was killed by the Grievers and Newt and the other Gladers retreated to the Cliff where the Grievers attacked them a second time. Newt and the other Gladers used their weapons to fight off the Grievers long enough for Thomas to type the code into the computer. Thomas eventually managed to type the code into the computer and as a result, a tunnel leading out of the Maze was unlocked and the Grievers were deactivated. Newt, along with the rest of the Gladers, used the dark tunnel to escape the Maze. The Gladers eventually made their way to a chamber where they confronted the WICKED agents responsible for creating the Maze. Before the Gladers could attack, however, Gally emerged from the shadows with a knife and killed Chuck. Thomas, angered at his friend's death, attacked and defeated Gally while a group of adults entered the chamber and killed the WICKED agents. The leader of the resistance against WICKED escorted Newt and the other Gladers out of the chamber and the Gladers and the resistance escaped on a bus. On the bus, the resistance told the Gladers that part of Earth was burned by overheating sun rays and many people were infected by a disease known as the Flare. The resistance also told the Gladers that they are heading for a burned out wasteland near the Equator called the Scorch which the Gladers must cross to find a cure to eradicate the Flare. After the bus reached its destination, a fancy hotel, the Gladers were fed with pizza. After dinner, the Gladers found a dorm with beds and went to sleep with Newt taking the bed next to Thomas and Minho's bunk.
Newt and the other Gladers were awoken by a disturbance: an insane group of humans infected by the Flare known as Cranks banged on the door trying to break in to the hotel, though the door was locked. Thomas also informed the Gladers that Teresa was missing. Thomas wandered the hotel in search of Teresa while Newt waited with the other Gladers in the dorm they were sleeping in. Thomas returned with a mysterious teenage boy he found in the room Teresa had been sleeping in. Newt decided to interrogate him. During the interrogation, the boy introduced himself as Aris and revealed that he was part of a group of female Gladers called Group B, much to the shock of Newt. Thomas also discovered he could communicate telepathically with Aris. The next day, a Glader named Winston informed the other Gladers about a man in the common room they dubbed Rat Man. A few minutes later, Rat Man told the Gladers about the Scorch Trials. Rat Man told them that he is a member of the organization WICKED and that most of the world's governments have disintegrated and the surviving governments banded together to form what would become the organization WICKED. He also reveals that the Gladers have all been infected by the Flare and they must reach a safe haven in two weeks where they will be given a cure and that they must use a Flat Trans to depart the hotel at 6:00 or they will be executed. After he was done explaining, Rat Man disappeared in a puff of smoke. Minho became leader of the Gladers following the discovery of a tatoo on his neck, which he washed off and the Gladers decided to get up early to avoid missing the Flat Trans. Newt also informed the Gladers that the Cranks have been driven off. At 5:00, the Gladers awoke and waited for the Flat Trans. The Flat Trans arrived an hour later, and Minho told Thomas to enter the Flat Trans last to make sure Newt and the other Gladers followed Minho. Thomas complied, and the Gladers entered the Flat Trans and were taken underground. Later, Newt and the other Gladers emerged to the surface and found themselves in the wasteland called the Scorch, where Thomas noticed an abandoned city a far distance away. Newt and the other Gladers trekked towards the abandoned city in hopes of finding food and water there. Halfway towards the city, two Cranks approached the Gladers and Minho questioned them about water somewhere in the city. They answered that they better think who is a friend and who the enemies are and they ran off. As the Gladers got closer to the city, they heard a shreik coming from a nearby shack. After drinking, Minho and Newt instructed Thomas to investigate the shack. When Thomas returned, he reported seeing Teresa. Minho and Newt immediately questioned why Thomas did not return with Teresa, but Thomas told him Teresa told him to part from her. The next morning, the Gladers noticed strange clouds in the sky and the weather was getting dangerous. Minho suggested they run to the abandoned city and find shelter before they got stuck in the storms. Upon hearing this, the Gladers quickly ran towards the city. During the rush, Minho was struck by lightning and caught on fire, but Thomas rescued him by pouring water on him. Shortly afterwards, the Gladers found a giant building they could use as shelter, and they entered to evade death in the storm. Once inside , Newt discussed with Thomas and the other Gladers their next move of action. Their conversation was interrupted by a hispanic leader of the Cranks named Jorge, who questioned the Gladers of their purpose. Minho insisted Jorge speak first since the Gladers outnumbered Jorge. Jorge took this as a threat and gave Minho ten seconds to apologise. Minho apologised, but without meaning, and Jorge attacked him. Minho apologised again, but was angered at Jorge's violent actions, and quickly attacked him until Thomas urged him to stop. A moment later, more Cranks showed up and Jorge asked Thomas to speak with him privately about the Gladers's business. After the private conversation, Thomas and Jorge returned to the room where Minho and the other Gladers awaited them and Jorge introduced the Gladers to a female Crank named Brenda and informed the Gladers and the Cranks about the Gladers's goal to reach a safe haven in two weeks to find a cure to eradicate the Flare and be freed of the organization WICKED's influence on them, but warned the Gladers that if they, along with Jorge and Branda, make it to the safe haven and there is no cure, Jorge will murder the Gladers. Jorge then led the Cranks and the Gladers to a tower to feed them. After lunch, Newt and the Gladers heard a crash coming from the lower floor of the tower and the Gladers and the Cranks rushed to evacuate. Newt, Jorge, and the other Gladers escaped the tower, but were seperated from Thomas and Brenda during the evacuation. Afterwards, Jorge led Newt and the Gladers through the abandoned city and eventually constructed a camp near the outskirts of the city. Newt and the other Gladers spread out to look for Thomas and Brenda after making the tent. During the search, the Glader Frypan reported seeing Thomas and Brenda taken prisoner by a small group of Cranks in an alley. The reported sighting angered Newt and the other Gladers and Minho immediately began planning out an ambush. Later, Newt participated in the ambush and fought the Cranks with the other Gladers while Minho freed Thomas and Brenda.Eventually, Newt and the other Gladers succeeded and defeated the Cranks and left with Thomas and Brenda. Before they could go further, however, Thomas was shot by Blondie, one of the Cranks, and Minho quickly subdued Blondie and the Gladers departed and returned to the tent with Thomas. Newt assissted the Gladers in removing the bullet friom Thomas's wound and Thomas quickly recovered and Newt and the other Gladers continued to the safe haven. On the outskirts of the city, the Gladers were confronted by Group B led by a corrupted Teresa. Group B took Thomas hostage and warned Newt and the other Gladers that if they followed the girls to their camp in the mountains to rescue Thomas, they will open fire on the Gladers with bows and arrows. Minho, aware of the consequence of attepting to rescue Thomas, did nothing to stop Group B from taking Thomas back to their camp and Newt and the other Gladers continued to the safe haven through the mountains. Sometime while in the mountains, Aris slipped away from the group unnoticed. After finally reaching the safe haven in a snowy valley, Newt and the other Glasders made an alliance with Group B to confront WICKED. A moment later, the Gladers were reunited with Thomas, Aris, and Teresa, now free of WICKED's corruption. Afterwards, several canisters emerged from the ground and strange monster emerged from them and attacked the Gladers and Group B. Eventually, Newt, with help from the other Gladers and Group B, destroyed the monsters. Shortly afterwards, a transport called a Berg arrived and Newt, along with the rest of the Gladers, Group B, and Jorge and Brenda, climbed aboard and escaped. Onboard the Berg, Newt and the other Gladers celebrated their success.
Newt meets again with Thomas at the start of the book. Thomas assumes Newt must've been through some harsh trial because he is more rebellious than before.
When they are taken to the rooms where they remove the Swipe, Janson announces the people who are not immune to the Flare and it's revealed that Newt is one of them, which causes Thomas to worry for his friend. Newt, though, doesn't seem very worried at all.
He is the only one along with Minho and Thomas who refuses to remove the Swipe, and they get a grip on Launcher weapons with the help of Brenda, which makes it easy for the four of them to run away and walk around the place.
Newt seems to be more angry than ever and has a fight with Minho. Thomas is afraid he is already losing his sanity to the virus. Newt picks up a letter and gives it to Thomas, telling him to only open when the time is right.
Newt runs away with Minho, Thomas, Brenda and Jorge in a Berg and they fly to Denver. The four last ones enter the city though Newt can't go in because he is infected while the others are immune. Thomas hears from Janson though that Newt was losing his sanity faster than the average Cranks. When they go back to the Berg Newt has left a note saying he was taken to a place where they hold Cranks and that it was for the best.
The group flies to the Crank Palace near Denver where they pay two guards to take them to Newt. At first they tell them Newt told them to 'get lost', but then they take the group to the Bowling Area, where Newt is. He carries a Launcher he stole from a guard and tells Thomas and Minho to go away, that he's found a group and they're going to break into Denver. He talks to Thomas with dispise. After a fight between Minho and a Crank from Newt's new group, Newt shoots the Crank and tell them to go once and for all.
When again inside the Berg, Thomas opens his letter to find Newt's wish:
Kill me. If you've ever been my friend, kill me.
Newt and Thomas meet again inside Denver, his mind already losing it's tracks and Thomas can see the wildness in his eyes. Newt tackles Thomas to the ground.
He tells him how he got his limp: in the Glade he tried to kill himself by climbing the wall of the Maze and jumping from there, but Alby found him and saved him.
He tells Thomas how he hated his life and wanted to die before he was past the Gone. He presses Thomas's pistol against his own temple and begs him to pull the trigger. Thomas says he can't but after Newt's brief glimpse of sanity, he shoots the friend on the head, killing him instantly.
Thomas later promises to himself never to tell Minho about what he had done to Newt.