ALERT! More spoilers for The Death Cure. I don't want to spoil anything for anyone, and be warned of the angst ahead- see a la page 250 kind of angst.
Newt hated the fact that there was no way he could comfort Thomas, despite how many times he tried to make his presence known. Despite his attempt to send any calming or positive feelings to Thomas or a calming hug to his shoulders, the fact was that Newt was dead and Thomas couldn't get over the fact that he was the one who pulled the trigger.
Newt wasn't sure when he first realized where he was. Early memories were of just Thomas and the immense desire to pull the teen into his arms. Slowly, the understanding that there were other people milling about in the world dawned on him, though not a single person acknowledged knowing that he was there. Not that he really expected any of them to know. It broke his heart every time Thomas cried himself to sleep or woke up from yet another nightmare. It was only slightly worse than Newt's fingers passing through Thomas' arm when he tried to soothe away the fear.
"Newt, God, I miss you so much," Thomas said to himself. He curled into himself under his pile of blankets as more tears coursed down his face. "Why did you have to be the one to get sick? Why couldn't I have been one of the control subjects? I should have taken better care of you when I had a chance. I should have never sent you into the experiment to begin with."
"I forgive you, Tommy. Me not being immune had nothing to do with you. I would have caught the flare one way or another. At least this way, I got a few extra years and I had you. Even for just a little while, it's better than nothing," Newt tried to convey back. He moved closer to Thomas, wishing that Thomas could feel him there. IT would have done wonders for Newt's mind and spirit if Thomas knew how much he really cared.
"I should have told you 'I love you' every day, Newt," Thomas whispered, as he slipped into a fitful sleep.
"I love you too, Tommy," Newt replied. "I'll find you again when you are old and grey, after you lived a full life. We'll haunt Minho, Chuck, and Gally together okay? We'll scare the klunk out of them for days and we'll especially get Minho back for all his crap and particular brand of sass." Thomas seemed to smile at the sentiment, in his sleep understanding what Newt was try to say that his waking mind couldn't hear. He placed and awkward kiss on Thomas' temple before drifting off around the paradise complex, alone and unheard.