Variable theory
This is an old theory of mine that I posted some years ago on winter-rowan. Not the winter-rowan you know, but the one from before my parents deleted my first account, that's how old this theory is. IIRC, I first posted about it after Fever Code released, in 2016, because Fever Code cemented it in my brain (It didn't get much attention, lol, pretty sure it now only exists in my brain. If anyone finds the original post, I'll add a link, but I had that blog set to unsearchable so it's likely lost to time).
This is mainly a book theory.
tl;dr: Thomas is the one who insisted he go in the Maze, and based his first interaction with Group B, the signs in the Scorch, Rachel being dead, and many other things, I think that WCKD never intended on sending Thomas into the Maze--but when he forced their hand, they did so, and used him as a Variable to further their experiment.
The variable theory is:
Thomas is a variable.
WCKD is very interested in his brainwaves, in him and Teresa and Rachel and Aris (we'll get to them a little later on). In Fever Code, it's heavily implied that they were never meant to go into the Maze; Thomas was the one who insisted, but with with caveat that he go in with his memories intact. As we know, Teresa betrayed him then and he lost his memories.
I'm betting WCKD was going to send Teresa and Aris at some point anyway--it's a good reaction test. But if you were a scientist studying the behavior of teens trapped in a Maze, wouldn't you want a control group of sorts? A group of teens not trapped in a Maze, to compare with?
Sending Aris and Teresa in makes sense. A reactionary point: how do these teens handle someone different from everyone they've known? (This would also make them Variables, but they're more permanent Variables than the Maze and the Scorch were).
(I would want to keep a few teens behind, personally. This is not an experiment I would ever run, or have anything to do with, but like. You have to know how the stressors of the Maze and Scorch are actually effecting them and for that you need a control group.)
So, it doesn't make sense to send them into the Maze. And Thomas wants to go because he wants to save his friends. IIRC (it's been a while since I read Fever Code in full), he's the one convincing everyone--including Teresa, Aris, and Rachel--to send them in.
Then in Scorch Trials, Group B kidnaps Thomas. Teresa is clearly supposed to make them think he did something to her, and they have been told to kill him. I don't remember rn if it's Thomas, Harriet, or Sonya, but one of them says that it might be a test: Maybe they are actually supposed to kill him. What WCKD wants is their reaction to him. A boy they don't know, who the new girl in their midst can't even stand to be around--what will they do? Will they kill him without letting him speak? Hear him out and then kill him anyway? Or, as they did, hear him and let him live?
WCKD would not actually let Thomas die; they needed him too much for that. But would others want him dead? How does Group A react, when Thomas is taken? (Beyond the initial yelling and threatening). What do they do when he's gone? How hard do they try to find him?
Add onto that that Rachel, Thomas's Group B counterpart, is dead (at the very least, we never see her again. With Gally still being alive I have my doubts on that one), and we know Gally was aiming for Thomas: If Thomas were 'dead' they could put him through all the tests and trials they wanted to study his brain, because no one would be looking for him.
This leads me to thinking about the 'Thomas, you are the leader' signs. We know Minho tells him 'yeah, you want it, take it.' And that Thomas takes a leader's role in talking with Jorge (which is likely because Jorge and Brenda would have both recognized him--he just dropped them off in the Scorch a few weeks ago. I'm probably giving Dashner too much credit here, but this meeting is very likely another of WCKD's tests, not just for the whole group, but to test Thomas alone as well.) Back to the signs: What would the rest of the group have done if Thomas took over as leader? Would Newt feel slighted and become bitter? What about everyone else: All of them have seniority over Thomas in this situation. Would they follow him in in open desert the same way they did in the Maze, especially after he ran ahead to get to Teresa without warning?
There is more, but this is getting long and I've got homework to do so I'll add it in a reblog later.
To conclude, for now:
I don't think Thomas was meant to be a participant in the Maze. Aris and Teresa I can understand, to some extent. Rachel and Thomas were likely meant to be the overarching control group: Both are around the estimated median age for their respective Mazes, intelligent, and were treated mostly the same as everyone else in the years leading up to the Maze.
