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Thomas didn't have to sit around and ponder what he felt for Newt. He knew from the moment he met the boy that he had a crush. He doesn't know what first drew him to the boy, but he knew what kept his interest going.
Newt is brave. He was only second-in-command in the glade, but he could easily run everything. Newt was funny, incredibly smart, and charismatic. And that smile could light up the entire glade. Plus Newt was the most beautiful person Thomas can remember ever seeing.
When they were working in the garden Thomas couldn't help but stare. Newt would be working away, sweat dripping down his face and his hair would be disheveled. Most of the time Thomas would be so distracted one of the other gladers would have to pick up the slack. Newt never seemed to notice Thomas' staring.
Newt was nice to everyone in the glade, but he was only close to two people. Those two people were Alby and Minho. At the beginning Thomas had been jealous of the two. Then at one point Thomas' jealousy kind of got out of hand and he thought that Alby and Newt were together. Thomas tried to latch onto that thought to get over Newt, but it only made him want the boy more. Thankfully, for Thomas' sanity, he later learned that Alby and Newt only saw each other as friends.
Thomas' infatuation goes a little bit farther after that. He starts to daydream about what it would be like to hold Newt. Would the boy like to cuddle a lot? Or would he like his space? What would holding Newt's hand feel like? Or what would his lips feel like against his?
Then Thomas started to get weirded out even with himself. How could he think this about a person he barely knew? He tried to get over his thing for Newt. It of course didn't work. Anytime Newt was around Thomas would be flooded with butterflies in his stomach. When Newt spoke to him he had to control himself from giggling. Thomas never got any relief. His thoughts were consumed with Newt even when the boy wasn't around.
Then Thomas tried to bargain with himself. Maybe his body was just confused. Before his memory wipe he probably liked girls. He may have even had a girlfriend in his previous life. Even Thomas didn't really believe himself. He liked guys, specifically Newt.
Thomas can admit he has a crush. Doesn't know how it all started, but he knows why it stays. It stays even though Newt doesn't know about his feelings. It stays even though there is a chance Newt will never return his feelings. Even when Thomas tries to ignore his feelings, his crush doesn't dwindle.
Thomas still loves him.