Part 2 to The First Cut is the Deepest.

You can read this without reading the first part, which is extremely graphic and gory.

Warning: This part of the story focuses more on emotional pain than physical, but there will still be graphic scenes, and some may find different aspects of this story triggering or disturbing.

Note: I recommend reading my stories through Archive of Our Own. Through AO3, I'm able to include media—links, pictures, videos, etc.

The Worst is Yet to Come

There was only so much Caitlin could do under these circumstances. She didn't have bandages. She didn't have an IV kit or sutures or anything to work with in the van. All she had was a partially conscious and emaciated Barry, lying naked on the floor of the vehicle. To make things worse, on the other side of him kneeled the Nazi-like doctor who had done this to him.

"Are there any immediate life threats I should know about?" Caitlin asked her stiffly.

"No," the woman said in her thick, Russian accent, "We were very careful not to do anything that would kill him."

"How thoughtful of you," Caitlin muttered as she felt Barry's pulse.

It was weak, but it was there.

"How can I help?" Dr. Holland asked desperately.

Caitlin didn't answer her. She was busy covering Barry with another blanket. He wouldn't stop shivering, and his breath kept hitching in his throat. Caitlin wished she at least had an oxygen tank in the van for him, but there was nothing. She continued to assess his wounds as she spoke to him.

"Barry? Barry? Can you hear me?"

Barry didn't look at her or respond. His eyes half open, he stared straight ahead at the ceiling of the van, his breathing becoming more and more labored.

Caitlin braced herself as the van took a sharp turn. She wished she could see what she was doing better. Being nighttime, the back of the van was much too dark for her to work.

His wounds were difficult to locate, mainly due to the large amount of dried blood covering his body. Caitlin pulled back the blanket to check his torso. Underneath all the bruising and dried blood, Caitlin was able to see that several of his ribs were broken. Barry whimpered when she gently palpated them, and she withdrew her hands away immediately, not wanting to cause him more pain.

Barry had suffered enough pain for a lifetime.

She was alarmed when Barry started taking short gasping breaths, each one more labored than the last. Caitlin opened his mouth to check his airway, but it was clear. She couldn't figure out why Barry was suddenly having trouble getting air into his lungs.

"Why is he breathing like this?" Caitlin asked the other doctor harshly, "What did you people do?"

"Nothing," Dr. Holland said honestly, "I can't think of any reason why he would have trouble breathing right now. We did all of our respiratory experiments ages ago."

Caitlin glared at her as she grabbed Barry's shoulders, lifting them up so she could slide her legs underneath him. Raising his head slightly was the only thing she could think to do to get Barry to breathe easier. When his respirations grew weaker, Caitlin started to panic.

"We need to get there now!" Caitlin shouted to the driver.

"Almost there!" Dig shouted back to her.

When they pulled up to STAR Labs a moment later, Barry was barely breathing. They threw open the doors to the van and were joined instantly by the others. They didn't waste time by grabbing a gurney. Without thinking, Joe scooped Barry easily into his arms and ran as fast as he could into the building. He tried not to focus on his son's labored breaths or the fact that Barry was completely limp in his arms. His only thought was getting him into the medical bay, where they could save him. Joe felt his stomach drop when he realized Barry's breathing had stopped altogether.

Felicity had been waiting for them at the lab. Joe ignored her questions when they all suddenly burst into the cortex. He rushed right past her, and once he was inside the med bay, Joe deposited his son onto one of the medical beds. Caitlin wasted no time getting to Barry's bedside. She tilted his head back gently to open his airway, and grabbed a bag valve mask, sealing it around Barry's mouth and nose.

"Cisco, come here and do ventilations!" she directed.

Cisco didn't hesitate to step forward and take the bag from her, squeezing it gently to force air into Barry's lungs. They all felt a slight relief when they saw Barry's bony chest rise. Cisco continued to provide steady ventilations for Barry while Caitlin attached oxygen to the mask and started listening to Barry's lung sounds with her stethoscope. She couldn't even get the diaphragm of the stethoscope to lie flat on Barry's skin. There was no cushioning between the bones of his torso, making the surface of Barry's chest bumpy everywhere she placed it.

The others didn't know what to do as they stood there and watched her work. Barry wasn't moving or breathing on his own, but his heart was still beating. To the others, though, it looked like they were trying to save a corpse. Barry was practically a skeleton, and he looked so…lifeless—with his limp body and half-open eyes staring in a way that was almost catatonic. It was like he was all but dead already.

"Do you want me to start an IV?" Dr. Holland asked her.

"No! You don't touch him!" Caitlin said angrily, "Someone just get her out of here! Let her leave. Lock her in the pipeline. I don't care! Just get her out!"

Roy grabbed a hold of Dr. Holland and led her from the room towards the pipeline. Dr. Holland didn't resist. She didn't even argue the fact that she had just helped them get Barry out of there. She just let Roy lead her from the room without protest.

Caitlin needed to figure out how to get Barry breathing on his own again, but to do that, she needed to find out what had caused him to stop breathing in the first place. She ran a quick ventilation perfusion scan, and her fears were confirmed.

"Caitlin, what is it?" Cisco asked, still squeezing the bag on the mask that was over Barry's face.

"He's having a pulmonary embolism," she said, quickly drawing up some medication, "I'm going to give him a thrombolytic to correct it."

Joe stepped forward to stand on the opposite side of the bed from her, looking down at his son. He grabbed Barry's cold, limp hand and squeezed it.

"Hang in there, Bar," he said to him as Caitlin injected the medication into Barry's other arm, "Stay with us."

Caitlin didn't wait to see what effect the medication had. She moved on to assess Barry's injuries now that she was in better light, while Cisco continued to provide ventilations for Barry.

"He has so many broken bones, and I'm sure internal damage. I'm going to have to take some MRIs and X-rays," Caitlin said, palpating Barry's abdomen gently.

"Here," Roy said, having reentered the room.

He handed Caitlin a stack of papers and some jump drives.

"That doctor insisted that I give these to you. She told me to tell you they were taken just this afternoon."

Caitlin looked down at the films urgently. She only looked at them for a moment however before she turned to Cisco.

"Stop giving the ventilations for a second," she told him, "I want to see if he can do it on his own now."

Cisco pulled the bag valve mask off Barry's face. They all held their breaths for several seconds before Barry finally took a shuttering breath on his own. They collectively let out a sigh of relief. Caitlin quickly placed a nonrebreather mask over the lower half of Barry's face to give him oxygen as he caught his breath.

Iris felt rooted to the spot as she watched things progress from a few feet away. She wanted to go and stand next to her father by Barry. She wanted to be close to him to provide whatever support she could, but she couldn't make herself move. All those weeks, she would have killed to go to Barry and comfort him, and now that she could, she couldn't make her legs work. It was as if she was afraid he would suddenly stop breathing again if she moved a single muscle. She was paralyzed by the fear she felt for Barry.

"Is he okay now, Caitlin?" Joe asked urgently, still squeezing Barry's skeletal hand.

"He should be stable now," Caitlin told all of them, "He must have had a blot clot somewhere. It most likely formed over one of his broken bones. When we moved him off that table, it caused the clot to break lose and travel to his lungs. I gave him a blood thinner, which helped it, but now we have to worry about internal bleeding. From the looks of his scans, it looks like he has some significant damage to his internal organs."

Caitlin looked through some of the papers Dr. Holland had grabbed from the lab. Her face darkened as she quickly read through some of the experiments that had been done to him.

"Oh, my God," she muttered, reading through one of the reports.

She looked like she was going to be sick.

"What did they do, Caitlin?" Cisco asked her.

She took a moment before answering him.

"You see all of these incisions here?" she asked them all, pointing at the unhealed cuts all over Barry's torso.

They all nodded.

"They're from surgeries that they've done to him," Caitlin said darkly, "Awake surgeries."

They all mirrored her disgusted look, completely horrified by what she was telling them.

Caitlin's eyes then fell on the center of Barry's chest.

"Oh, my God," she said again, touching the sutured incision lightly—tears sprang to her eyes when she saw it, "They didn't…"

"What is it, Caitlin?" Joe asked her angrily, "What did they do to him?"

"They…" Caitlin choked, pressing a hand to her lips for a moment before continuing, "They performed heart surgery on him, too."

They all looked at her in shock and then at Barry. Sure enough, he had a long, sutured incision down the front of his chest.

"They cracked his chest?" Oliver asked angrily, "While he was awake?!"

Caitlin nodded, blinking back tears. She touched the incision again, still not quite believing it was really there. Barry was shaking violently under her touch. His every muscle was tensed in fear as he continued to stare straight forward.

"Let's get some clothes on him," Joe said, looking pitifully at his son.

Cisco stepped forward to help Joe get some sweatpants on Barry. The scientists had stripped Barry of any dignity he had and dehumanized him in every way. They all felt like it was the least they could do to clothe Barry now and respect the little privacy they could give him.

Barry didn't move or speak as they maneuvered him to dress him. He was awake, though, his eyes still staring blankly forward. Every time one of them touched him, however, he would tense slightly and a small whimper escaped his throat, indicating he was at least partially aware of his surroundings.

The pants didn't even remotely fit him. They probably could have fit two of Barry into the pants with how loose they were around his waist. At least he was covered now, though.

Caitlin did her best to assess Barry while touching him as little as possible. Her eyes raked over Barry's torso again. Most of the incision sites were sutured already, but some were still left open. She would have to close them or they would be risking infection.

"I have to stitch up a few wounds on him, yet," Caitlin told them quietly, "You can all stay in the room if you want, but you should probably not stand too close to him."

They all nodded and backed away towards the wall. Caitlin grabbed her things and set them next to Barry's bed. Before making the first stitch to a cut on his abdomen, she spoke gently to him.

"Easy, Barry," she soothed in a hushed voice, "It's just me. It's Caitlin. I'm not going to hurt you. I'm just going to stitch you up, okay?"

Barry didn't seem to have heard her. He was still staring blankly forward, shaking slightly as his breath continued to hitch in his throat. He tensed when she applied iodide to the wound. When she made the first stitch, Barry gasped.

"It's okay, Barry," she said to him, "It's just me. You're okay."

Barry suddenly turned his head to look at her, panic in his eyes as they focused on her face. Finally, he moved.

He grabbed her arm painfully to stop her from touching him, and he used his other arm to pull himself as far away from her as possible, grimacing in pain with the movement. Everyone rushed forward instinctively to help the young doctor, but it only caused Barry to panic more when he found himself suddenly surrounded by so many people.

Barry started to scream hysterically when they touched him. He thrashed violently, trying to escape their grasp.

Joe and Oliver tried to grab hold of Barry's thrashing legs, trying not to apply not too much pressure to where they were broken while also trying not to get kicked in the process. Caitlin and Cisco tried desperately to hold Barry's arms.

"Barry, stop, it's okay," Cisco shouted to him, just as the arm he was holding down managed to break free and make contact with the side of his face.

Still yelling hysterically, Barry started to vibrate, desperate to get out from their hold. In an instant, he managed to wrestle free from them and flash to the other side of the room. He didn't get very far on his broken legs, however, and collapsed only a few feet away. He screamed and clutched at his legs, his panic seeming only to increase with the renewed pain. Before they could move towards him, Barry tried to run again, disappearing again with a burst of speed. They heard a clatter as he knocked over a surgical tray, and they quickly turned to see him huddled in the corner of the medical room.

Barry was no longer shouting now. He sat whimpering in the corner, one hand supporting him against the cold floor, the other still holding onto one of his injured legs. His eyes darted about the room, trying to make sense of his surroundings. He stared at all of them in fear. His breathing was rapid and shallow, and he still had the needle and thread dangling from his stomach where Caitlin had only made one stitch.

"Barry," Joe said softly, cautiously kneeling down a good few feet away from him to give him space, "Barry, it's me. It's Joe."

Barry didn't change. He stayed huddled in the corner, watching them vigilantly in case they tried anything.

"Bar," Iris said gently, kneeling down next to her father as she outstretched her hand, "It's okay, we're not going to hurt you."

Barry tried to withdraw further into the corner, but he was already tight against it. When Iris brought her hand closer to him, Barry's arms flinched up, shielding his head. She pulled her hand away, completely heartbroken. Barry thought that she was going to hit him. He really thought she was going to hit him. Iris's heart tore in two.

"You're safe, Bar," Joe said desperately, "We're just trying to help you, okay? You're safe now."

Joe inched a little closer.

"No!" Barry cried, cringing away from him, squeezing his eyes shut tight.

It killed Joe to see Barry so afraid of him. He was completely terrified, and none of them could do anything to help him. Joe and Iris slowly got up from the floor and backed away from him.

"What should we do?" Joe asked, standing back with the others.

"We can't get through to him right now," Oliver said, looking at Barry with solemn eyes, "We'll have to restrain him."

"Are you crazy?!" Iris snapped, "After what he's just been through? We can't put restraints on him!"

"Do you have any better ideas?" Oliver sighed, "He's going to keep trying to run, and his legs are completely shattered. He's just hurting himself."

They all stood there a moment, thinking as they looked down at Barry huddled in the corner. He was sobbing now, staring at them in fear. He knew they would move in on him eventually, and there was nothing he'd be able to do about it, and that absolutely terrified him.

"Okay," Caitlin said reluctantly, "I guess we don't have a choice."

She walked over and pulled out several cravats.

"I don't exactly keep restraints on hand here, but these should work just fine," she said, looping the small strips of medical cloth, "They should be soft enough."

She gave one to Oliver, Joe, Dig and Cisco. They each decided on which of Barry's limbs they were each going to take, and after a nervous nod at each other, the four men moved in. Barry started screaming instantly, but they crowded around him anyways.

"No!" Barry cried, "Please! Please! No!"

He fought them hard, trying to escape them again, but they held him down, each slipping their restraint over one of his wrists or ankles. They managed to half carry, half drag the screaming man back over to the bed, where they wrestled with his limbs, tying them to the frame of the bed. When he was secured, they all stepped away from Barry right away, trying not to crowd him any more than they had to.

Barry pulled violently against the restraints in desperation, but it was futile. He started to cry.

"Oh, God," Barry sobbed, "Please! Please, no more! I can't take any more! No more surgeries! Please!"

"We're not going to hurt you, Barry," Caitlin choked, tears forming in her eyes as Barry begged.

Barry kept tugging desperately against the restraints. They were soft, but his already scabbed over wrists and ankles were starting to bleed from the pulling.

"Please," he continued to sob, "No more tests. Just please. Please stop. I can't do this anymore. I can't do this."

Their hearts broke to see him this way. Joe started to cry, feeling guilty they had to do this to him. He knew restraining Barry was only going to traumatize him further, but they didn't really have any other options.

After several minutes, Caitlin moved to sit next to Barry again. She touched his stomach gently as he whimpered.

"Barry, I'm so sorry, but I have to close this up," she told him reluctantly, "I'll try to go fast for you."

Without waiting for a reply, Caitlin resumed stitching Barry up. He started to yell again, but she kept working, trying to go as fast as she could. Guiltily, she moved onto the next cut. It took her nearly an hour to finish stitching all of his wounds, a painful hour during which Barry screamed and cried the entire time, and the rest of them stood by helplessly, unable to comfort him.

When Caitlin was done, she backed away from Barry as quickly as possible.

"That should be it for stitches, but there's still so much more to do," she told the rest of them shakily.

Barry sobbed as he laid on the bed. Even though they weren't locked up on the other side of a glass wall now, they all still felt the same helplessness when they were unable to comfort him.

Iris approached the side of the bed with tears streaming down her face. Barry stared at her fearfully as she took his hand. He flinched at her touch and slightly withdrew his hand, but she held it anyways.

"Barry," she said gently, "It's me. It's Iris."

Barry continued to give her the same terrified look, his breathing growing more ragged.

"Iris," her dad said, standing next to her, "I know you want to help him, but right now, I think you're just scaring him more."

"I can break through," she said earnestly, "I think I can break through to him."

"Not right now," Joe said gently to her, "Right now, he just needs to heal."

Reluctantly, Iris released Barry's hand. She turned and hugged her father, crying into his shoulder.

Barry went back to staring at the ceiling, still shaking violently. He was starting to hyperventilate now.

"I think we're overwhelming him," Caitlin told the others, "I still have to rebreak and reset quite a few of his bones. It's going to be brutal, and I think it might go smoother if we're not all in the room."

They all took one look at Barry and couldn't help but agree with her.

"I think it's about time we get going anyways," Oliver sighed.

Felicity looked incredulously at him.

"What do you mean?" she asked, "We can't leave now. We only just got Barry here."

"We've been away from Star City for too long," Oliver insisted.

"We can't leave, Oliver," Felicity persisted, "Barry needs us."

"Barry needs his family," Oliver corrected, "We've done all we can do for him. Our presence here isn't going to help him now. Trust me, I want to stay here with Barry, too, but we have responsibilities back in Star City. We can't afford to spend another night here."

"I can't just leave him," Felicity said, "I can't leave without knowing he's going to be okay."

Oliver sighed.

"Okay," he said, "You can stay here if you want to, Felicity, but the rest of us really need to get back."

He looked at Diggle and Roy, who both nodded at him before leaving the room. Oliver paused by the doorway. He took one last sad look at Barry, and then looked at Caitlin and Felicity.

"Keep me updated?" he asked sadly.

They both nodded. Oliver let out a heavy sigh, and then turned and left the room. The rest of them also filtered out, leaving just Caitlin and Cisco in the room to work on Barry.

Joe, Iris, and Felicity all sat in the cortex in silence. It wasn't long, however, before they all could hear Barry's screams resume in the next room. Even from out in the cortex, they could hear the sound of bones being rebroken and snapped into place.

It seemed to go on forever. Iris didn't know how she still had any tears left. She thought her tear ducts would have dried up by now, but no. A continuous stream of tears streaked down her face as she listened to Barry scream over and over again. She looked down and saw that her hands were shaking. This was almost as horrible as it had been sitting in the room next to him watching those scientists torture him with their unspeakable experiments. She just wanted the screaming to stop, and after nearly two hours had gone by, finally it did.

Cisco emerged from the room. He looked exhausted, and his eyes were red and wet.

"We're done," he said shakily, "You guys can come in now."

They all walked over to the doorway. Cisco hesitated.

"Just…don't make too much noise," Cisco advised, "No sudden movements, and whatever you do, don't touch him. He's exhausted, and we're trying to get him to calm down now."

Cautiously, they entered the medical bay. Caitlin was laying a blanket over Barry, who did not look good at all. His face was gray, tear stains etched into his cheeks. His eyes were red and staring open wide as he shook uncontrollably.

"We're done for the night," Caitlin said to them in a hushed tone.

She looked sadly at Barry's traumatized face.

"I need him to calm down enough to sleep now. He needs rest."

"Shouldn't we clean him up first?" Felicity whispered.

Barry was still covered in blood and filth.

"I would like to," Caitlin said regretfully, "But I don't want to do more than what's absolutely necessary right now. He really needs sleep."

Barry let out a gasp. His breathing was heavy and irregular.

"Please," he said in a small voice, "Please, just leave. Don't hurt me anymore. Please."

"Barry…" Caitlin said softly.

"I feel pain," he breathed, "I'm a person."

"I know, Barry," she said gently, "I know. There won't be any more pain now. Not tonight."

Barry started to sob, tears streaming down his face. They all stayed silent and sat down in chairs a good distance from the bed. They wanted so badly to help Barry, to comfort him, but they knew that the best way to do that now was to keep their distance.

Everyone sat silently for a long time while Barry cried. Eventually, his sobs died away, and his exhaustion won over his panic. His eyelids slowly started to droop as he fell asleep. He fought it, snapping his eyes open again every couple minutes or so, but eventually he wasn't able to fight it any longer, and Barry fell into an uneasy sleep. They all were careful not to make any noise. Even the slightest sound seemed to cause Barry to snap awake instantly.

They all decided then that it was best they leave the room. They didn't want to risk accidentally waking him up when he had just finally gotten to sleep. They all left and sat out in the cortex, where they could still see Barry through the med bay window.

As a whole, they looked like a complete mess. They looked exactly like how you would expect a group of people who had been taken and held hostage for weeks to look. Cisco was now sporting a black eye from where Barry had hit him, and Caitlin's arm was bruised from where he had grabbed her.

Iris's eyes were red and puffy. She seemed to have finally ran out of tears, but her throat was still sore, adding to the feeling that she could start crying again at any moment.

"I don't know what to expect," Caitlin said sadly, "The psychological damage that's been done to him is going to be much harder to treat than the physical damage."

"His mind is shattered," Joe whispered brokenly, "He…he doesn't even seem to recognize us."

"He's in a lot of pain," Caitlin explained, "Barry's mind is still locked in a prolonged fight or flight mode. It's clouding all other thoughts, his survival instincts taking over."

"Well, how do we fix it?" Iris asked desperately.

Caitlin shook her head sadly.

"It's not going to be easy," she told them, "It's not like simply flipping a switch. Barry's in a chronic state of panic right now. He has been for weeks. Barry's mind and body have been panicking nonstop for weeks. It's not going to turn off easily, not with everything that's been done to him."

"Maybe if he just gets some sleep," Joe sighed, "Those scientists never let him sleep. That, alone, is enough to cause someone's mind to snap."

"Sleep should help," Caitlin agreed, "He should do better once his mind finally allows his body to rest. He's not used to resting now, though. He's used to endless pain, twenty-four hours a day. It might take a while to retrain his mind to…to establish a sense of safety."

They all nodded sadly and looked at the floor, not knowing what to do—how to help.

"You all should get some rest, too," Felicity finally said, looking at all of them, "I can watch out for him tonight if you guys want to go home and clean up and eat something."

"I'm good here," Joe said, looking at Barry through the window.

His heart clenched every time he looked at Barry's bruised, gaunt face. Barry's thin limbs were all still restrained to the bed frame as he slept. It was a heartbreaking sight. He didn't even look like Barry anymore.

No one else seemed to want to leave either. After weeks of sitting in a room wondering where Barry was and what was happening to him, none of them wanted to let Barry out of their sight now.

"Joe," Caitlin said, "I think you and Iris should go home and get some sleep. There's nothing more you can do here tonight. I don't want to leave Felicity alone, so I'll stay with her here. We'll look out for him, and you can come see him in the morning."

"I don't want to leave his side," Iris said stubbornly.

"You have to go home at some point," Felicity pointed out to them, "It's probably best that you do it now, when Barry is still out of it. He's going to wake up later and need you, and it will be better if you both are well rested."

It took quite a bit of persuading, but eventually Joe and Iris reluctantly agreed to go home, leaving Caitlin, Cisco, and Felicity to stay at STAR Labs to care for Barry.

When they pulled up to their house, Joe and Iris were shocked to see 'do not cross' tape on their front door. Then they remembered; the CCPD had been looking for them. It would only make sense that they would have searched the house. Joe would have to contact them eventually. He still didn't know what exactly he was going to tell them, but that wasn't one of his priorities at the moment. Now, all he could think about was Barry and how much he was struggling right now.

When they crossed the tape and walked through the front door, they couldn't help but notice how unreal this all felt. They were home. The house felt too…normal. It was as if the last few weeks had never even happened.

Except they did.

Every time either of them thought about Barry, how terrible he looked, how emotionally broken he was, they felt sick to their stomachs.

Joe and Iris both showered, but they were both feeling too sick to eat anything. It's not as if they were starving anyways. Although the food at the military facility hadn't been good, at least there had been plenty of it.

"What's going to happen now, dad?" Iris asked her father miserably.

He didn't need to ask to know what she meant.

"We're going to get him back," Joe answered firmly, "It might take some time, but we're going to get our Barry back."

"I don't know how a person can ever come back from this," she said hopelessly, "What those people did to him…It's just too much. He's so far gone…"

"Barry will be Barry again," Joe said surely, "We just have to give him time. The worst of it is over now."

Iris shook her head absently.

"Somehow, I don't think that's true…"