Major spoilers for The Death Cure ahead. The Maze Runner franchise is coming to an end after four years and three movies, and Thomas, who began as a hero running around the glade in The Maze Runner, has made it to the end of his journey. But it's not an end that comes without a cost. Fans that know Thomas know that he's a self-sacrificing type of hero, which means there's a very high likelihood that Thomas dies in Maze Runner: The Death Cure. Luckily, Thomas escapes death a few times in the final Maze Runner film, but others are not so lucky.
The Death Cure is by far the most dire Maze Runner film yet. In this film, there is no glade, no home base to retreat to, and only a handful of allies. On the bright side, now out of the Maze, Thomas doesn't have the Grievers to fight. That said, the threats to his life have multiplied. In The Death Cure, Thomas comes head to head with Cranks (zombies), WCKD operatives, and murderous rebels. Luckily, Thomas has his trusty gladers Newt (Thomas Brodie-Sangster) and Frypan by his side, as well as newfound allies Brenda (Rosa Salazar) and Jorge (Giancarlo Esposito), while they face the dangers of the outside world in an effort to rescue Minho (Ki Hong Lee). Thomas, despite being an enthusiastic "act first, think later" type of hero, survived the film relatively unscathed (save a gun shot and the odd scratch), but his friends weren't all so lucky.
It turns out that not all the kids sent to the glade were immune to the Flare virus after all. Newt gets infected early on in the film, and, though Thomas is desperate to keep him alive so they can get him a cure, Newt doesn't make it. Ava Paige (Patricia Clarkson) also meets her end after Janson (Aiden Gillen) becomes infected and shoots her to make sure he gets Thomas. Thomas' blood, it turns out, is the key to the cure, and Janson wants to own him to own the cure, and thus have power over who gets to have access to it or not. With some help from Teresa (Kaya Scodelario), Thomas defeats him (RIP Janson), and the two escape with the one sample of the cure Teresa has made. Unfortunately, Teresa doesn't make it, which means Thomas loses two of his closest allies and friends in the span of about 30 minutes. Before she dies, however, Teresa gives Thomas the cure, which could be a clue as to where Thomas' story is going to go next.
Though there are no plans to create more Maze Runner movies, if they did, there's definitely more story to tell. Because the movie ends with Thomas alive (and pumped full of cure-worthy blood), it leaves the door open for him to eventually return to the Flare-infected world and help cure the virus. The movie ends with him, now fully healed, on an island with other escapees and immune children, where they plan on establishing a new society. The last shot is of him eyeing the boat they came on, holding the cure in his hand.
Thomas survived the Maze, he survived the Scorch, and even helped destroy WCKD. To the delight of many fans (especially all the Brenda-Thomas shippers out there) Thomas is now free to live his life in peace with his friends by his side. But, of course, if there's one thing Thomas is known for, it's his desire to help. If he can do something, he does it. Even if that means traveling back to a hellhole and risking his life to cure the world. Sure, Thomas is alive, but for how long — that's up to the audience's imagination.