Thomas had fallen for Newt at the very beginning. When he saw the boy on the fateful night of his arrival, among all these people, his heart had beaten faster.
Newt had fallen for Thomas, when he ran into the maze or at least he realized it the moment the pain in his chest faded, when Thomas had made it out alive.

The two boys were always oblivious to each other's feelings, which would cause them to feel anxious and sad,  worrying about what the other felt. Those times, Newt usually cried himself to sleep, while Thomas would escape to a far corner of the forest to let it all out.

Naturally the rest of the Glade had realized the pain it was causing them. After all they noticed visible changes. Newt  had dark shadows under his eyes and didn't make as much conversation as he used to. Thomas on the other hand was even worse off. Every time they saw him leaving the forest he returned with fresh wounds, mainly in his knuckles, which were even more obvious covered in bandages.
As time passed, he even lost his sarcastic 'charm', but every time one of the others tried to approach the subject he dismissed them

Finally Minho, Alby, Frypan, Chuck and even Gally devised a plan to get those two together. "Those two are a couple of wrecks" Gally says. "We have to get them to confess their feelings for each other" Chuck replied. "Yeah, but how?" Alby asks. While Minho had an idea in mind, Frypan was already coming up with a plan.

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