10/10/14: Revised and edited as of today.

Hey everyone. This is my first fanfic for The Maze Runner.

Warning: Please only read this fanfic if you have finished all three books, as it contains a lot of spoilers. DO NOT read beyond this point if you have not finished the trilogy yet. If you choose to disregard this warning, it is entirely your choice.

Now, to business. I would like to clarify that in this fanfic, Newt, Minho, Teresa, Thomas, Gally, and Frypan are all alive and well. As this is a fanfic about Thomas and Teresa, Brenda was the one who died saving Thomas. This is after the events of The Death Cure.

Although Thomas thought he shot Newt, it shall be revealed that that was not the case.

Please enjoy.

Disclaimer: I do not own The Maze Runner in any way, shape or form.

Discovery

He thought he was done with WICKED's mind games. He thought it was all over; the Trials, the deaths, the doubts about who he could trust.

He should never have trusted WICKED.

Then he wouldn't have been staring into the eyes of a ghost.

Thomas had seen countless of his friends die. He had held Chuck in his arms as life ebbed away from the boy. He had seen Brenda push him out of the way of a falling chunk of rock, sacrificing her life to save his. He had been asked to shoot one of his best friends in the head.

Or so he thought.

WICKED had revealed that Newt, one of the boys that Thomas had first come to know in the Maze, was not immune to the Flare. Thomas felt himself shudder as he thought about the Flare; the terrible disease that thrived in the human brain, that destroyed a person's humanity and turned them into less than animals. Newt had started the journey along that path, and Thomas and Minho had watched helplessly as their friend had slipped away from them.

Newt had asked Thomas, in a final, desperate gesture, to kill him. Shoot him in the head and put him out of his misery.

Let him leave the world before he lost his sanity, went past the Gone. Went to a place from which he could never come back.

And Thomas had done it. With one last burst of energy, he had pulled the trigger.

Newt was dead.

Until that morning…when everything had changed.

"Here again?"

Teresa walked forward to sit beside him, her legs hanging off the edge of the cliff, facing the ocean. Thomas had already known it was her the moment she spoke. She was the only one who knew that he always came up here in the early morning to look out over the ocean.

"I was remembering the time before the Flare-it was devastation, but the world would have pulled through. If only the Flare hadn't spread, everyone would have been alright," he murmured quietly. And I would never have been forced to be part of WICKED's plans, he finished in his head.

Teresa was silent for a long time. "You know I got the Swipe removed," she said after a while, her voice low. "I got my memories back; and I saw how the Flare had been released into the world to contain the population.

I remember these four people who took care of me; Mark, Trina, Lana and Alec. They all lived before the sun flares. Alec got them out, along with a couple of others, when the flares hit. They travelled overland, all the way to the Andes. That's where they stayed. And then, one day, WICKED decided that there were too many people, and too little resources.

They had developed the Flare as a means of population control. They expected it to shut down the brain quickly, provide a fast death. They thought that it would keep what remaining resources from finishing too fast. Of course, they didn't give a damn about the people they were condemning to death."

Thomas wished he had punched Rat Man harder. He may not have been the one who had ordered the release of the Flare but he must have been involved.

"But then something happened that they hadn't planned for," Teresa continued. "The virus mutated as it spread from person to person. The first few died quickly, but as it spread, faster and faster, the symptoms took longer to show, and by the time people started quarantining the infected around them, they had already caught the virus.

Alec decided that they had to leave, and they ran away after their settlement was destroyed by WICKED. The same thing happened to my family. But, by the time they left, my parents had caught the Flare, and they started losing their humanity."

Teresa's voice trembled. "They thought I was a devil, because I wasn't sick although I got hit by one of the Flare darts. They abandoned me. Trina and the others found me when I was running from Cranks. They took me in and looked after me."

Thomas looked at Teresa, and noticed tears in her blue eyes.

"But they weren't immune, Tom. They caught the Flare, just like everyone else. I could see it happening. Sometimes Trina's eyes became darker, and she looked at me with this hungry look, like she wanted to eat me. When her sanity returned, she would apologize to me, crying all the time.

Of course, at the time I had no idea what was going on. All I knew was that something had happened to my parents and the same thing was happening to them and it terrified me. They held it off as long as they could, searching for a way to save me. WICKED left the East when they saw what happened. Trina and Mark…they knew that they had to get me to go with them.

They got me to a Flat Trans, just as the last WICKED member went through. Mark told me that I was special, that someday I would do something to help the world get rid of the Flare. I could see him fighting off the madness. I could see it in his eyes, almost on the brink of craziness, holding on just to help me. He scribbled a note to WICKED, telling them I was immune. He told me to go through the Flat Trans, and to be brave."

Teresa's voice shook ever-so-slightly, and her dark blue eyes glimmered. "There were a couple of Cranks who wanted to fight WICKED. Mark told me to run. I stopped just at the last possible minute, just before Alec crashed the Berg into the building. I remember seeing them-Mark and Trina-hugging, as tightly as possible. That was the last time I ever saw them. I still can't forget about it, Tom. They knew they were going to die; but they accepted that and they died so I could be safe."

Teresa leaned her head on Thomas's shoulder and he put his arm around her waist. It was meant to be a purely platonic gesture, but that wasn't how Thomas felt anymore. The very first moment they had tumbled into their new paradise, Thomas had been too exhausted, too emotionally drained to do anything. But now…now something in him had changed towards his best friend.

Teresa broke his musings. "I never told you this Tom but…I'm really sorry about Brenda."

Thomas's jaw clenched tightly, his eyes closed as he remembered Brenda. Brenda, who had stuck with him through the Scorch and on their search for a cure for the Flare. Brenda, who had cheered him up, supported him, who had been just as tough and kick-ass as Teresa.

"Brenda chose to save me," Thomas finally spoke. "Just like Chuck did. I'll never forget them, but I can't spend my life mourning them either. They wouldn't want that. I have to accept and move on. The dead can't come back."

That was when Minho had come running up the cliff yelling at the top of his lungs. He stopped when he saw Thomas and Teresa sitting together, but he didn't even tease Thomas about it. He just ran towards them and yanked him up.

"What's wrong, Minho?" Thomas asked. The boy's eyes were wide with shock and…was that hope? "You have to see," his friend replied, his voice full of an unnamed emotion. He turned and ran down the cliff, with Thomas and Teresa hot on his heels.

He stopped right beside the mess hall, at the place where they had come through the Flat Trans, leaving the Flare-infected world behind them once and for all. A group of boys were huddled around something-a person. Frypan was leaning down over him, fingers checking for a pulse. He looked up, and beckoned Thomas forward.

Thomas knelt down beside Frypan, and his knees nearly buckled when he realised who was the person who was lying on the ground, exhausted. A face he had thought was lost to him forever.

The boy smiled weakly. "Tommy," he whispered.

And then Thomas knew, without a doubt, who it was.

Newt.

Thomas was staring at Newt's face blankly. Minho had taken charge, telling them to move Newt to a bunker. Minho and Thomas had carried Newt to their own cabin, which both of them shared, and got him some food.

Newt had sat up, and was just finishing sipping his water. Thomas had been staring at his face since he had first seen the boy. He was pretty sure Minho was doing the same.

His mind kept replaying the last time he had seen Newt-the boy had begged him to kill him, pleading with him. And, finally, Thomas had granted that wish, although it had choked him with grief and despair.

But Newt was sitting here, perfectly fine.

It had taken all of Thomas's courage to tell Minho what he had done to Newt. He had been fully expected to receive a punch and he was going to let Minho go at him. After what he had done, he didn't think he would be able to lift a finger in his defence.

To his complete surprise, Minho had looked at him for a minute and in that one look Thomas knew that Minho was letting him know that he had understood. Minho had given him a brief nod and then left him to his thoughts.

But how on Earth was Newt sitting in front of them-eating and drinking and breathing?

Thomas had no clue what to make of it. He was half convinced that he was in a dream. Or WICKED was just testing them. Again.

After all he had gone through, he wouldn't be surprised.

Newt seemed to understand what was going on in their minds. He drew out a folded piece of paper from his pocket and gave it to Thomas. Thomas's heart contracted. He remembered the last few times Newt had left them notes…he wasn't exactly eager to get another.

If Newt was going to ask Thomas to kill him after Thomas had just got him back, Thomas was seriously going to lose it, Flare or no Flare.

Newt rolled his eyes. "It's not a bloody suicide note, Tommy. Just open it."

Relieved, he opened it. His eyes at once flashed to the name of the letter writer and a shiver ran up his spine. Her name was familiar, even though Thomas had never met her. Thomas read the letter aloud:

WICKED Headquarters

4th October 2320

Dear Thomas,

I know you are shocked and confused right now. I know what you must be thinking. But I assure you, Thomas, this is not a Trial. WICKED is finished. I don't know if you realize, but it has been three years since you left this world once and for all. Three long, hard and difficult years, that you have been spared.

With all our efforts, we have not succeeded. The Flare has mutated, and spread faster and faster and the matter is beyond our hands now. As much as it horrifies me to say it, the world has succumbed to the Flare. The Flare, at least, brings with it now the merciful bliss of death, allowing us one grasp of hope. The human ace has been wiped out.

At this moment, I am the only person alive who has a minimal grasp of sanity, apart from Mr Newton. But not for long-even as I write, I feel the madness beginning in my brain, and I see insanity and death speeding towards me. I only wish that I will soon leave this world, and my suffering will not last long.

I don't know how long it will take but I know that one day there will not be a single person alive in the world, except for the two hundred or so people with you, Thomas. What I must ask of you now is, perhaps, the most difficult task we have ever given you; begin the human race anew. Learn from the mistakes we made and start a new civilisation.

I am sorry that we put you through such hardship-in the Maze, the Scorch, and even after. I am sorry that you suffered so much more than any child has a right to suffer, and I am sorry that you witnessed things that no child should ever have to witness. All I ask is for your forgiveness, and the promise to begin the human race again. I wish you the best.

All throughout history, leaders have made mistakes and civilisations have fallen; but greater ones have sprung up on their place. I place my faith, and the faith of the world, in your hands Thomas. I know that one day, you will accomplish the task that we have set for you.

I don't know how history will view us, but now all I can say, is that WICKED had only one purpose, and that was to save the human race, at any cost.

And for that sole reason, WICKED is good.

Chancellor Ava Paige

There was a pin-drop silence when he finished reading.

Thomas looked up to see the same shock and horror that was on his face mirrored on Minho's. But Newt's expression held only the terrible pain of grief and sadness. Thomas couldn't imagine what Newt must have been through, but he knew it must have been terrible, having to witness the long arduous process first hand and see the world destroyed.

Thomas finally broke the silence that stretched between the three of them. "Newt, how-I mean, did you know what-"

Newt interrupted him. "Yeah, I saw. I saw every single thing from the start to the end."

Thomas and Minho looked at each other in confusion. "I wasn't there," Newt explained. "After the Scorch, they took me away. They said that Thomas and Teresa were the Final Candidates-whatever that meant-and they said they needed to put in place a final variable to see how Thomas reacted."

"They wanted to know how Thomas would respond if he had to kill one of his closest friends. All those times you thought you were talking to me-yeah, that wasn't me at all. You guys were talking to a hologram of me. Remember when we thought all those rescuers were killed?"

Thomas remembered that all too well; the grotesque swelling and smell of the bodies, the way their faces had been blue in death, tongues hanging out. The thought of it made him want to throw up.

"Yeah, they can manipulate the smell and sight of the image as well. None of them were actually killed. It was just a bloody hologram."

"Wait a shucking minute," Minho interrupted.

"You mean to say that when we thought you were going crazy-you actually weren't even going crazy at all? You weren't even there?"

Newt nodded. "I'm Immune to the Flare, just like you guys. But I could see everything you were saying to 'me', and what you were doing."

"So you saw what-"

"I don't judge you, Tommy," Newt broke in. "I knew you had to do it. It must have taken a lot of courage on your part."

"Thanks," Thomas muttered.

"Anyway, I kept the hologram in place until you guys drove off and then I vanished it. I've been at WICKED headquarters for the past three years; trust me, I put up a hell of a fight at first, destroying stuff and refusing to take part in any of their plans before Ava came to speak to me."

"She convinced me to help," Newt looked defeated, suddenly. "Fat lot of good it did in the end. She sent me through the Flat Trans, before she shot herself. She said she didn't want to live as a Crank."

Thomas felt his heart explode with relief. Newt really was back-it wasn't a Trial, and it was over.

They were finally free.