Thomas was standing over Newt's cranked-out dead body when the realization that he could have prevented all of this from happening hit him. He was backing away when he noticed that Brenda was running up to him. "I could have prevented all of this if I would have gone with W.C.K.D, and Teresa, when they invaded the Right Hand's base camp," Thomas said with a hint of sadness in his voice. "If you did they would have killed you to create the cure, and besides we wouldn't have made it this far without you," Brenda said as she tried to comfort him. "Brenda, you know as much as I do that isn't true!" Thomas said. "No, without you we would probably be at the Safe Haven right now, but I would be without the love of my life," Brenda said while fighting back the tears that were on the verge of overflowing, meanwhile all he could do was stand there speechless. "I love you, Thomas! That's right in the short time that we have known each other I have fallen in love with you. I was just hoping that we could have had more time together." Brenda said as she moved closer to Thomas.
"I love you too, Brenda! I was also hoping that we could have more time together, but Jorge is like a father to you, and I wouldn't be able to live with myself if what happened to Newt were to happen to him or anyone else!" Thomas said before he kissed her on the lips. "I'm going with you!" Brenda said. "No, Brenda I want you to get Minho, Jorge, and the rest of the immunes out of the city. I can't lose you, and if your safe I'll have even more of a reason to make it out of this alive." He said before letting her out of his embrace. "Okay I will, but you have to promise that you will come back and find me once you have killed Janson, Ava, and the traitorous shank of a woman that is your sister, Teresa," Brenda said as she backed away from him. "I promise that I will!" Thomas said before he took off running toward W.C.K.D Headquarters. Brenda was so distracted by the retreating form of the man that she loved that she didn't see Frye, Minho, and Gally run past her and drop to their knees next to Newt's corpse.
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After Thomas secured the door he heard a voice saying "I see that your sister's plan actually worked!" he raised the gun he had while turning to see that it was Dr. Paige talking to him. "Is it true? Newt? Could I've saved him?" Thomas asked while crying. "You could save us all!" she replied while nodding her head causing him to drop the gun he had aimed at her. "It's okay." Dr. Paige said reassuringly. "Just promise to leave Brenda, and the other immunes alone," Thomas said. "I promise that no harm will befall her or your friends while I'm in charge of W.C.K.D!" Dr. Paige swore just before a loud bang was heard echoing throughout the halls of the Building.
When both she and Thomas looked down they saw a bloodstain on her chest that was rapidly growing. Thomas turned around to find Janson holding a literal smoking gun while slowly walking toward him. In one quick motion, Janson injected Thomas with a tranquilizer dart once he got close enough to him. "Oh Thomas, You should have run." was the last thing Thomas heard Janson saying before he passed out.
(Line Break)
Thomas was awoken by the sound of explosions off in the distance, to find his sister drawing enough blood to make the antidote for one person. "Do you know what this place is, Thomas?" he turned his head to find that it was Janson asking him that question. "It's a lifeboat, that was supposed to provide safety to those who could afford it, while the world around us went to hell," Janson said as he walked away from the window behind Thomas.
"How much longer?" Janson asked Teresa while Thomas struggled to break loose. "It's almost done!" she answered with her back toward him. "Why don't you just kill me?" Thomas asked. "Kill you?" Janson answered as he started to explain himself. "No, we don't wanna do that. We're gonna take special care of you. We'll keep you alive, just long enough to extract your blood and make the cure." Janson said just barely avoiding a headbutt. "Of course, there's not gonna be enough for everyone, hard choices have to be made," Janson says as he grabs a syringe from the operating table. "In time, the Flare virus will burn itself out. The only question is...Who will be the ones left standing." he states as he walks towards Teresa and yanks the vial from her.
"A future of our own making!" he says while pulling up his sleeve, and revealing that he himself was infected. Before he can inject it into his body Teresa cracks him over the head with a becker causing him to fall over just long for her to start helping Thomas get loose. "Teresa!" Thomas yells as Janson throws her halfway across the lab. After breaking free Thomas spears Janson through the glass wall behind him, and a fight in sues. The fight ends with Janson pulling a gun on Thomas just before an RPG rocket hits the floor knocking him off balance.
Thomas and Teresa use this as a chance to run and hide in another lab where there are two cranks in a cage. "We need to get out of here!" Teresa says as Thomas realizes that he's been shot in the abdomen. "What's wrong?" She asks causing him to turn and show her.