A/N: OK hi guys. First of all, I didn't think anyone was actually going to read my stories, so when I saw the emails saying people had been reviewing it, I was shocked! Just as an FYI, the story is complete, I had just wanted to put out the first couple chapters and see what people thought! So by the end of today, maybe tomorrow morning, the full story should be posted! I just wanted to say thanks guys! I'll answer your comments when I can, thought I have to run to classes soon! Thanks again!

BTW, I changed the time line in this story like a gazillion times, so I'm hoping I caught all the changes that needed to be made, but if I didn't, please feel free to let me know and I'll fix it!

Present time, Finch & Shaw

"Can you zoom in on the license plates on either of those vehicles?" Finch requested of The Machine. As the plate numbers became clear, Finch jotted them down. "Could you run the plate numbers and see to whom they belong?" As the AI started the process, Finch turned to the two women in the room with him. Shaw had a triumphant look in her eyes, and even Grace looked happy.

"I'm so happy for you, Harold," she said as she took his hands in hers. "John is alive!"

"Yes...or at least he was five weeks ago," he added. Shaw glared at him.

"We need an extraction strategy," she stated. Finch shook his head.

"I agree with you, Ms. Shaw, but until we know where he is being held, we cannot make any such plans. We would have nothing to go on, no idea what escape routes to take, nothing." Shaw's mouth slanted, but she knew he was right.

They sat in silence for a few minutes while they waited for The Machine to work through the databases trying to find out who the cars belonged to. Finally the monitor flashed, indicating The Machine had found something. All three of them leaned forward, looking at the findings. Harold tapped some keys on the keyboard, but after a few moments his shoulders slumped as he read what was on the screen.

"It's a shell corporation linked to an empty account. I can set up a program that can run the name and figure out who is behind it, but it will take time to program it, and then more time to let it run." The disappointment was clear on his face, and Grace leaned down and wrapped her arms around him from behind.

"No need," Shaw said with a cold look in her eyes. "That's ISA." Finch looked at her.

"Ms. Shaw, are you certain?"

"I worked with them for years, Harold. Pretty sure I know one of their fake corporations when I see one. Step aside. I know how to find where they're holding Reese."

July 15, 2016

The door opened and John sighed in exasperation. It was Dr. Murphy, followed by six men armed to the teeth. "Well Mr. Reese, how are you feeling today?" The question was answered with silence, as it usually was.

The past few weeks had been a steady routine. The doctor would come in a few times a day, always guarded by ISA agents. They would let him up to use the bathroom, they would give him some food, ask him how he was doing, and then leave. John found out the hard way that if he tried to get away or fight at all, there was a stun gun with his name on it just waiting to be used. He hated being cooped up in the room, but he had to admit it; he was tired. After being shot multiple times by Samaritan ops, getting a concussion from the butt of a rifle, and the multiple encounters he had with the stun gun, he was simply tired. He also knew that they had given him sedatives. Not enough to knock him out usually, but just enough that he was more lethargic and couldn't fight back as well.

His wounds had actually healed quite well, but he still had the occasional twinge of pain whenever he moved a certain way. His shoulder had healed enough that they had removed his arm from the sling and promptly secured it to the bed via velcro as well.

The doctor continued checking John's charts while the men took up their usual positions by the door and by his bed. After a minute, Control walked into the room. John raised an eyebrow. She hadn't come in since last week, when she had thrown the pictures onto his bed.

Flashback to a week prior

"John, I know this is hard to accept," Control said as she help up the pictures in front of him. He sat in stoic silence, looking her directly in the eyes and not at the photos in her hands. "But Harold and Shaw are dead." John didn't even dignify her with an answer. She sighed and rubbed her hand over her face. "Mr. Reese, the facts are in front of your eyes. One of the agents you disposed of on the roof got word to his friends before he died, telling them they had seen Harold leaving the roof of the building next to you. They met him at the bottom of the building. He never stood a chance. Ms. Shaw was with Detective Fusco when a Mr. Blackwell cornered them. Ms. Shaw was killed, and Detective Fusco has been in critical condition for a few weeks. He just got out of the hospital, and he took his son and they moved out of the city. You're alone, John." John took in a deep breath.

"You're wrong," he stated simply.

"Excuse me?"

"I. Don't. Believe. You." He enunciated every word. His eyes never left hers for a second.

"We have cold hard facts, Mr. Reese, I-"

"Photos can be faked," he interrupted. "Stories can be told, evidence can be manipulated."

"Mr. Reese, I-"

"No. You have tried to convince me that I failed in keeping everyone I love safe. I know what it feels like when you've failed to protect someone you love. I'm not feeling that now. So you can take your 'evidence' and leave me alone." Control had said nothing. She simply turned and left the room, taking the pictures with her.

End Flashback

John stared at the woman as she walked towards him with a device in her hands. He thought about making a snarky remark, but decided she wasn't worth his time or energy. He shifted his gaze so he was staring blankly at the wall until she walked into his line of sight, forcing eye contact once again.

"Mr. Reese," she greeted. He gave no indication that he had heard her, so she just continued. "I think it's high time we let you out of those restraints for good, don't you?" He tilted his head.

"Does that mean you're admitting I was right and letting me go?"

"Heavens no. Call it a show of good faith. We need you in shape to go out on missions, which you won't be if you're tied down in bed. However," she continued as she held up the device in her hands; it almost looked like a gun. "There are a few stipulations." She walked to the side of his bed while fiddling with the instrument. Two men put their hands on John's shoulders to restrain him should he try to fight. He gave a slight wince as his almost-healed shoulder groaned under the new pressure. Control placed the device against John's right forearm and pulled a trigger. There was a sharp pain, but the only sign John showed that he felt it was a slow blink of his eyes. Control had a tissue and she wiped off the bit of blood that appeared on his arm before turning to the guards. "Release him." They all stood still, not wanting to untie the man who was obviously dangerous. "Do not make me repeat myself," she warned.

As the velcro straps being were undone, John simply sat there. As soon as the last strap was removed though, he burst into action. Or at least he tried to. He barely got one punch in before a terrible pain went up his arm and through his body. He collapsed to the ground with an agonized groan, holding his arm. Finally the pain subsided and he looked up at Control.

"I think you need to work on your definition of 'good faith,'" he muttered through his teeth. She stared impassively at him as she held up the gun-like instrument, not bothering to acknowledge his comment.

"You've just been injected with a state of the art tracking chip, complete with perimeter guard. I can see every move you make, watch you everywhere you go. If you go anywhere you're not supposed to, if you do anything I don't approve of, I can simply press this button and...well, you just experienced the low setting." John glared at her.

"You're no better than the Samaritan agents," he said with quiet rage. If you didn't know him, you'd think by the volume he spoke and the tone of his voice that he was just making small talk, but for those who knew him, those who knew what he was capable of knew that that tone of voice meant you should run the first chance you get. "You claim to be keeping the world safe, making it a better place, but at what cost? Imprisonment, torture, lying; the only thing that's different between you and Samaritan are your names." She blinked, then continued on like she hadn't heard him at all.

"The door to this room has been equipped with something akin an electric fence one would use to keep a dog in the yard, only it's got a bit more of a kick to it. If you manage to get past the door without collapsing, the electricity will only continue to increase in voltage. I think you can imagine what happens when it reaches full potential." Without saying another word, she turned and walked out the door, followed by everyone else in the room. The door shut, and John heard the electronic lock click into place. He rubbed his arm absentmindedly as he looked around, trying to find anything that would help him get out of his current situation.

July 16th, Present Time

Over the course of the next 24 hours, John had tried every possible way he could think of to get out of his room, but every time he even went near the door, it would send a shock through his body. His arm was in an almost constant state of cramping now from the amount of times he had been shocked, and he was now sitting on the bed, giving his body a rest from the torture. He stared at the ceiling, trying to figure out how he could get out of here, or at least try to get a message to Finch. He sat that way for a few minutes before he heard the electronic lock being opened and in walked Control. She was holding a stack of clothes which she tossed to him. "Put these on," she ordered.

After he came out from the bathroom with his new clothes, Control beckoned him forward. "We're going on a walk," she informed him. He was skeptical and hung back. "Don't worry, you won't be shocked when you come near the door this time." Still, John didn't come forward. She sighed and motioned for two of the men who accompanied her to bring Reese with them as they walked out of the room. They walked behind John while two other men got in front of him, boxing him in. They marched out of the room like that with Control leading the way. They led him down a hallway and down a flight of stairs until they reached a door, which Control opened. John walked in and stared at the scene around him.

A series of walls had been set up strategically, and the room was dark. Reese realized what it was a split second before the door behind him closed. He was in a training room. A shot echoed around the room as something hard struck the wall right above his head. He instinctively ducked around the corner, pressing himself against the hard surface as he reached for his gun that was no longer at his side. He cursed and went into a crouch, staying low to the ground as he quickly made his way through the maze, never staying in one spot for more than a few seconds. He rounded one corner and came face to face with someone who raised a weapon at him. Almost without thought, John grabbed the gun and yanked on it, bringing the threat closer to him, then shoved the gun back in the face of the man, dropping him to the ground.

He grabbed the gun from the unconscious man, quickly patting him down for any other weapon that he could use but found nothing. He brought his newly-acquired rifle against his shoulder, keeping an eye out for anything that moved.

It was dark in the room, but his eyes adjusted quickly. He continued to creep around the corners, his breathing quiet and his senses on high alert. He was aware of almost every noise around him, every shifting of the shadows. He thought he saw something out of the corner of his eye, causing him to duck out of the path of a bullet just in time. It wasn't quick enough to avoid the bullet completely though. He hissed in pain as his left arm burned from the recent contact with the bullet. He turned and fired his own weapon, smiling a grim smile as he heard a cry of pain and a crash as the person who had shot at him fell. John could imagine them clutching at their leg in agony. He didn't know how many hostiles he was up against, but he knew there had to be more than two.

A few minutes passed with no action of any sort. As John made his way around one corner, he came to a sudden stop. Five men were standing there with weapons raised and aimed directly at him. His gun had automatically raised in defense, but he stopped and lowered it.

"I'm not playing your game anymore," he stated coldly. "If you want to have your men kill me, go ahead. I'm not going to work for you." He heard the shift of the guns as the men waited for orders.

He was expecting it, but he still fell to his knees as a stronger surge of electricity coursed through him. He fell against the wall after the currents stopped flowing, taking in deep breaths to try and even out his labored breathing. His arm was still spasming when a door was opened and Control stormed in. She barked at a few of the agents to go pick up the men John had taken out, while the rest of them stood behind her, waiting for a command. She stared at John, anger flashing in her eyes.

"Do your worst," John dared with a smile as he held his arm against his chest to try and control the shaking. She sat in silence a moment longer.

"Get him up," she finally ordered harshly. John was pulled to his feet, then dragged out into the hallway where they zip-tied his wrists together behind his back. Control stood in front of him. "You could have easily taken those men out back there," she pointed out. "Why didn't you?" John smirked.

"ISA needs all the help it can get," he replied simply. "I was only doing you a favor." Control said nothing, but jerked her head, indicating she wanted to start moving. They shuffled him down the hallway and got to the stairs, intending to take him back to his room to let him stew a few more days.

As they started going up the stairs, the lights flickered, then turned off all together. Flashlights were flipped on as they heard pounding steps coming down the stairwell and John was shoved against the wall as the fighting ensued. Through the searching flashlight beams, John could see that one of the ISA agents was standing in front of him, gun drawn and obviously trying to protect the prisoner. He knew he didn't have a lot of time, so as quickly as he could, he bent his knees and slipped his bound hands around his legs, bringing them to the front. He hit the man in the back of the head, knocking him to the ground instantly.

He turned and yanked the door open, running as fast as he could down the long hallway. He had just reached the end of the hallway and was about to turn the corner when the worst shock yet wracked it's way through his body. He couldn't stop the cry of pain that wrenched itself from his mouth as he fell to the floor, gripping his spasming arm. His momentum from running threw his falling body into the wall, dazing him. He felt hands grabbing him roughly, then heard a sickening slicing noise and pain exploded on his arm. He groaned in agony as he felt something digging around in his arm, but finally his body took mercy on him and he passed out.