Author's Notes: I am currently posting this story over on my AO3 account and when I reached The Autobot Files, I noticed these old files (They're like ten years old, holy crap!) had a bunch of typos in them. So, as I am posting this fic on AO3, I am also editing each chapter as I go. You may notice the chapters of this fic have been taken down on here. As I edit, I'll be re-posting the updated chapters here as well. There will not be any extra content in this edit, just attempting to make the fic look better. I'll try to edit around one chapter a week if I can. Thank you to both old and new readers!

The Autobot Files

By: Ty-Chou aka Ghost of the Dawn

File #001 - Harm

A large, heavy crate came up the hallway, carried by an Autobot roughly its size. He stumbled for a bit as he tried to maneuver around and then kicked at the closed repair bay doors.

"Hey Ratchet," Brawn called. "I got your package. Open up!"

"Oh, I got it!" called a feminine voice from inside and the door slid open.

"Where do you want this?" Brawn then asked.

Ratchet's voice came from somewhere in the back. "Crystal, see if you can find some space for that."

Brawn could barely make out her figure over the crate he carried as Crystal's small form looked around the cluttered bay. "Oh um... okay."

He could hear her skirting around, moving things and pushing others out of the way. "Put it down over here."

Brawn did his best to peek over to see where he was going and slowly made his way to the open space made for him. He could see Crystal's dubious expression as he moved past her.

"Do you... need some help?" she asked.

"Nah, better not get in the way, Princess," Brawn replied. "It's not heavy for me, it's just big. But it just might squash you."

Once at his destination, Brawn set down the massive cargo. He made it look easy, but with the heavy thunk it made, it indeed sounded extremely heavy.

"Is that my package?" Ratchet asked as he came up. He had a certain twinkle in his optics that was similar to a kid on Christmas morning.

"Straight from Cybertron courtesy of Cosmos," Brawn said as he patted it. "Just for you, Doc." He rotated his shoulder joints. "Carried it all the way from outside."

Ratchet looked eager to rummage around inside, but glanced back at Brawn as he began to pry it open. "How are your joints holding up?"

"They've still got another good battle in them, no worries, Doc."

Satisfied, Ratchet turned his full attention to his package as he lifted the lid.

Right then, Wheeljack poked his head in. "Ooh! Is that the new shipment of parts from Cybertron?"

Ratchet slammed the lid down protectively. "Repair bay gets first call on them, you know that."

Wheeljack sidled up to him, his fingers twitching in anticipation of touching what was inside. "I just want to see what you got is all..."

Ratchet didn't look convinced and continued to keep it closed while Wheeljack fingered the lid. "You always say that and then sneak yourself whatever you want."

"I just need one power converter, that's it," Wheeljack finally admitted. "It doesn't even have to be the best one. And maybe a coolant filter and some extra wiring and-"

Ratchet countered his list and the two broke into an argument over who deserved what and who got the best of the last shipment. Crystal watched them silently, unsure of what to do. She glanced over at Brawn across the crate. He was a bit different than the other Autobots she had seen. Smaller, more bulky and compact. He smiled at her, friendly, with an "You better get used to it, this happens a lot" type expression.

"I'm going to do a full inventory of the package and THEN we'll see what I can afford to let you have," Ratchet said with finality.

"Fine," Wheeljack relented with a sound in his voice akin to a sigh. "But I better not just end up with scrap."

As Ratchet was finally able to inspect the contents, Wheeljack turned to Crystal. "How are you feeling? Still got that thing?"

He poked her in the back and Crystal instantly flinched away from the touch.

"Yup, still do," Wheeljack confirmed. "Think we should take a look at it, Ratchet? It's been two days."

"Give it a bit more time," Ratchet responded, his head in the open crate. "Going from organic skin to metal skin is a rough transition in itself. It takes a while to get used to."

Wheeljack placed his hand flat on her back and Crystal shrank away from it as if he had poured ice water down her back.

"Stop it," she whined.

"What does it feel like?" Wheeljack asked, intrigued.

"Like needles and sandpaper. Like all my skin has been rubbed raw."

"And it feels like that everywhere?"

He reached out to touch her arm, but Brawn grabbed him first.

"She said she doesn't like how it feels. Stop harassing her."

Wheeljack finally found the grace to look guilty. "Sorry, I was just curious."

"You always have to push it a little too far," Brawn accused then folded his arms. "Well, if there's nothing else for me to do here, Doc, I'm gonna get back to work."

Ratchet waved him off, mumbling something as he was fully occupied with his new toys.

Brawn turned his attention to Crystal. "The name's Brawn. If this one," he threw a thumb at Wheeljack, "gives you any more trouble, you call me, okay?"

Crystal's face lighted a bit. "Okay."

Brawn gave one more warning look to Wheeljack and then marched out of the room and down the hall.

Wheeljack glanced at Crystal who seemed to be in a better mood now that he was on Brawn's list.

There was a heavy snap as the crate lid fell on top of Ratchet while he was half inside the container. Crystal gasped and hurried to help him. When Ratchet was free, he kicked Wheeljack out of his repair bay so he could conduct inventory in peace.

Crystal stayed with him, even though Ratchet had made it clear several times that she was free to leave the med bay after her daily diagnostics check and could go anywhere in the base she wanted. But she never wanted to go anywhere. Even though the medical officer caught her peering down the hall several times, she didn't want to leave the room. If he got after her too much, she would retreat to her small cubbyhole in the back corner out of sight and remain there silently for the next few hours. Ratchet surmised her desire to not be touched was part of the reason she didn't want to go out, but he wasn't sure if it was the entire reason.

After going through that routine for two days in a row, Ratchet decided he would not say anything today and see where that got him. He was getting a bit put out by the fact that the entire base had wordlessly established him as this girl's babysitter until she was ready to meet the world. But there was nothing that could be done. He may have been a bit annoyed to constantly be sharing his once coveted solitude, but he didn't have it in his spark to boot her out. Yet. He would wait to see how a few more days of this would make him feel.

He looked up when he noticed Crystal was watching him intently as he unpacked the crate.

"Do you... want to help?"

She brightened up instantly. "I would love to! What can I do?"

He gave her a tight smile as he straightened up. "Handle each item carefully and place them on the table so I can inventory everything."

Crystal nodded, seeming delighted to have something to do. Ratchet thought it might be good to continue giving her jobs after this. If she wasn't going to leave the med bay, at least he could get some work out of her.

The crate was almost as tall as her chest. Crystal had to really reach to grab the different pieces of equipment until it started getting lower. Then she gingerly climbed into the box and began handing Ratchet the pieces on the bottom. He paused in the midst of moving parts as a red light flashed on his shoulder.

"What's that?" Crystal wondered.

Ratchet was still, as if listening to the sound of an invisible voice. "Prime's sending out a unit. Decepticons are about."

Her optics grew wider. "What are they doing?"

Ratchet went back to work. "Not sure. Stealing energy is what they're usually up to. I hear they're getting pretty low. That makes these missions more dangerous because the Decepticons are getting desperate."

Crystal tipped her head at him as she handed him the next item. "What do they need it for?"

"They need it to live. We all do, even you. We need power to keep our bodies running and our weapons charged. Not to mention our base."

"Where do the Autobots get theirs?"

"Some, from Earth's government as donations, but a majority of it we harvest from your natural resources. We have solar and hydro power conductors as well as the thermal energy we gather from this volcano. We don't have an over surplus. But it's enough to keep us powered comfortably. When the Decepticons go after it, they usually end up destroying more energy than they steal."

"Sounds quite counterproductive of them," Crystal commented.

"And now they're paying the price," Ratchet agreed.

The crate was empty and he offered her a hand to help her out. Then he looked around his repair bay.

"Well, if a confrontation is coming up, I'm sure we'll have a few damaged bots coming in eventually. Would you mind cleaning up while I take inventory?"

Crystal nodded and went right to work. Ratchet was right, she was downright pleased to have something to do.

She was more than happy to do anything he asked of her. This also gave him the free time to look over his lovely new collection of parts. Every once in a while Ratchet would look up from his inventory to check on her. Crystal appeared to be moving slower every time he gazed in her direction. It made Ratchet wonder if she was doing it deliberately. Having something to do gave her mind something to think about instead of dwelling on her current situation. Maybe she was trying to stretch it out so she could keep busy. Ratchet could allow that. She needed time to adjust to her new body and, if she was being active, it was good therapy for her, so he let her be.

"Ratchet?" Crystal's voice asked softly.

"Yeah," he responded automatically without looking up.

"Um, I still don't feel very well. Is there maybe...?"

Ratchet looked up at her. "The same stuff as before?"

She pressed her lips together and nodded.

He swung his chair around, eager to get this conversation over with so he could finish his inventory.

"We ran your diagnostics test this morning and everything looked normal. Give it one more day and if it's still bothering you, we'll see what we can do tomorrow, okay?"

"...Okay."

"Hey, hey! Look who's back!" announced a rowdy voice accompanied with a smiling face.

"Jazz!" Crystal exclaimed as she hurried over to him.

"Hey babe!" Jazz grinned as he came into the room. "Sorry I've been away these past two days. Had to go on a mission. Came back as soon as I could."

She squeaked as he swept her up into a tight hug without warning. Then he put her down when he felt something was off. Her body was trembling in his arms.

"Crys, you okay? You're shakin'."

There was a tremor in her voice as she pressed her face into his side. "I just really missed you."

"Aww..." Jazz pulled her closer. "I'll always be back for ya. Don't worry your little head about it, okay?"

He pulled back and despite the fact that she was still shaking a bit, she smiled at him. "I know."

"So," Jazz then said as he grabbed her hand. "I heard you haven't really been out of the med bay at all. Do ya... wanna go for a walk with me or something? I figured maybe if you had someone to go with..."

Crystal moved back, shaking her head and pulling her hand out of his.

"Not ready, huh? Well then," Jazz hopped onto one of the tables and patted the place next to him as an invitation to sit.

Crystal climbed up to join him. Ratchet could hear the conversation, but kept his optics on his work.

"So uh... you really knocked ol Prowl on his can two days ago."

Crystal frowned. "He deserved it."

Jazz tried to give an understanding smile. "Did he really?"

"Yes," was the final answer.

Jazz looked down at his feet as he swung them back and forth. "You know, he took that really hard. He pretty much just took off out of the base and never came back."

"He disappeared?" Crystal asked, genuine worry in her voice.

"Well, not so much disappeared. He responds to his radio if you call him, but he insists he's working on something and he's not coming back until he's done." Jazz looked up at her. "I think he's trying to give you some time. Are you still mad at him?"

"I have to be," she responded in a small voice, looking down in her lap.

Jazz folded his arms. "And why exactly do you think you have to?"

"Because... if I'm not mad at him then everyone else will be. And I'm the only one who should be mad at him."

It took a moment for Jazz to figure that out. Had she picked up on that much? That there were those who were angry with Prowl's decision and those who may want retribution for her if she didn't claim it herself. Was she protecting him from everyone else's negative feelings by punching him out in the control room?

Then Jazz frowned as he noticed something. "Crys... you okay? You don't seem..."

He couldn't find the words to describe it. He just had a feeling when he saw her sitting there, hunched and looking very uncomfortable, that something was wrong.

She looked up at his face, almost a desperation in her optics, as if she had been waiting for someone to ask her that. As she opened her mouth, an alarm sounded.

Ratchet got up with a sigh. "Looks like our boys are back from battle already and my med bay's gonna be full. Jazz, I need to ask you to leave so you'll be out of the way. If you want to take..."

Crystal was already backing up toward her corner of the med bay. She was still adamant about not leaving.

Jazz just smiled. "I'll come back later when it's less busy."

He managed to slip out just as the injured Autobots were brought in. Ratchet was instantly at the door, ordering different patients to different tables and lining them up according to the severity of their injuries. Luckily, while there were several patients, no one had any serious wounds.

'But it's still going to take me all night to finish with these,' Ratchet thought with a frown. 'Especially with Wheeljack out for the count as well.'

He noticed the inventor, who had gone with the unit, had sat himself on a table and was attempting to repair his own mangled hand. He certainly would be no help until it was repaired. Ratchet was on his own for now.

"So, how'd it go?" Ratchet asked Ironhide. The red Autobot had taken a direct shot to the knee joint, but insisted on limping in under his own power. Ratchet knew if he didn't cover that wound soon, Ironhide would get bored and go limping around the base, making it worse.

"How'd ya think it went?" Ironhide grinned. "We clobbered them good and they ran off again."

"But not without getting in a few good shots, I see," Ratchet frowned. "I think their aim is improving."

Ironhide waved him off. "Lucky shot," he insisted.

"Don't get too cocky, Ironhide," Optimus Prime counseled as he sat next to him on the table. There was a good sized hole in his shoulder compliments of Megatron's cannon. Exposed wires sparked their dislike for being blasted. "The more we starve their energy supply, the more desperate they become. I worry one of these days Megatron is going to do something very drastic and if we're not careful, we'll get sucked up in it."

"Yeah, yeah," Ironhide mumbled.

Optimus poked at his exposed wires.

"Don't pick at it," Ratchet warned.

Their leader slumped.

As Ratchet tended to Ironhide's leg, the red Autobot leaned over and talked in a low voice. "How's the kid doing? She still hanging around or what?"

"She's in the back somewhere. She just hides when I'm working," Ratchet grumbled. "I can't get her to leave. I'm not sure if I should give her more time or what? I don't know what kind of behavior to expect for something like this."

"Meh, the kid was a bit off to begin with if you ask me," Ironhide shrugged. "But I don't blame her for feeling outnumbered around this place."

"Give her more time," Optimus said. "If there's no change after things slow down around here, we'll see what we can do."

"Right," Ratchet nodded as he pulled out his welder. "I've got a med bay full of injured Autobots. I'll worry about those first."

Several hours later, he was still fixing minor injuries. None of them needed immediate attention, but there were a lot of them and a few required some intricate, time-consuming repair work. Of course, not every Autobot wanted to stay in the med bay for hours on end waiting their turn, so Ratchet had to keep leaving the bay to hunt down the next patient, which took even more time.

It was the next morning when Ratchet stood up after leaning over Hound's open chest cavity for almost an hour and straightened his back.

"There, good as new. There shouldn't be anything rattling around in there anymore. I wish you would quit off-roading. I'm sick of cleaning out all the dirt and nature before I'm able to repair anything."

Hound shrugged as he sat up. "Can't help it, it's in my alt mode. Thanks, Ratchet."

The medical officer tiredly waved him off, knowing full well his requests were never heeded.

Optimus Prime entered as Hound left. He gave Ratchet a moment to stretch out his aching joints before speaking.

"Everyone's been tended to?"

"Until next time," Ratchet muttered. "Those Decepticons better give me a few days' rest or I'll slag them all myself."

"Agreed," Optimus nodded. "I worry we're getting more careless with our confidence. We come back with more injuries than they do almost every time. But the reason I'm here is because of what you said earlier." He shifted as if it was something he would rather not think about. "I would like to see how Crystal is doing and be present during her diagnostics if you haven't done them already."

"No I haven't been able to do anything but repairs." Ratchet glanced towards the back of the med bay. "She's overdue, too. It's been over twenty-four hours. I'll get her."

He waded through the different parts and equipment scattered around to get to the back corner. Crystal's body was found laying on her cot and Ratchet immediately thought she didn't look right at all. She was curled up facing the wall, muscle cables clenched tight and her body trembling.

Millions of years of medical training were not required to see that something was definitely wrong. Mentally going through all her data in his head, Ratchet reached out to her as he quietly said her name. His touch wrenched a cry of pure anguish from her and Ratchet instantly pulled away.

"Crystal, what's wrong?" he demanded, looking her over.

"It... hurts... everywhere." Crystal's voice came out in strangled gasps. "My skin... like fire.."

Ratchet looked like he was going to attempt to pick her up and then thought against it.

"Crystal, I need to touch you," he said.

"No!" she managed to scream. "Don't! It hurts!"

Ratchet was frozen for a minute, but then pressed his mouth into a firm line. As quick as he could, he grabbed her shoulder and forced her on her back. Crystal couldn't hold back the scream of pain and struggled as he pulled her chest cavity open and turned off all her systems. Her body slowly stopped thrashing as the light in her optics faded and she fell offline.

Ratchet sat back on his heels, shoulders sagging with relief now that the immediate crisis had passed.

"What happened?" Optimus demanded. He had seen the entire display.

Ratchet sank further, gazing helplessly at the small body in front of him. "I... I don't know..."

.

Two hours into the systems diagnosis and Ratchet and Wheeljack still had no idea what had gone wrong. Several wires and cables were plugged into Crystal's body as data scrolled through the screen. Every system, every set of code was checked and rechecked. But everything looked to be running the way it should, completely by the book. Ratchet had gotten so frustrated with the situation Wheeljack had insisted on taking a turn because the medic was too frazzled to think straight anymore. Instead, the white Autobot paced in agitation around the room, going over the same equations in his head, trying to figure out what he had missed.

Optimus Prime was present as well. He had ordered the med bay quarantined and no one else was allowed in for any reason until the problem was solved. The Autobot leader was clearly uncomfortable with the situation as well, but was handling it better than Ratchet, who looked like he was down to his last nerve.

"Prime," Ratchet said, his voice hoarse with stress. "I can't go on like this anymore. Even if we fix this problem, neither Wheeljack nor I are qualified to keep monitoring this poor girl's health. We need Perceptor. Programming is his specialty. Prime, you have to get him down here. The sooner the better."

Optimus leaned against the wall and watched Wheeljack hunch over information screen.

"That is not an easy request to make. Preparations for only one soldier to come to Earth is very uncommon, not to mention expensive. There are going to be questions as to why exactly we need him."

Before Ratchet could push his argument, Wheeljack cried out and triumph.

"Found it!"

Ratchet was instantly standing behind him to witness the discovery himself.

"Look here," Wheeljack said, pointing to a batch of code. Optimus Prime had no idea what it meant, but Ratchet nodded in understanding.

"We turned up her external stimulation sensory to better replicate the high sensitivity of human skin. I didn't think we had it up too high to be a problem, but what happened is that there was a break from the stimulation impulses to the main processor. Crystal could feel the stimulation, but the system controlling her sensory perception wasn't getting the signal at all. It kept thinking the sensory output was too low and kept trying to compensate by turning it up.

"Eventually it got so high that every little touch became magnified a thousand times over. It was so intense it was painful despite the fact that she wasn't physically being harmed."

Ratchet slammed his fist on the table, startling the other two Autobots in the room."And I let her stay in that condition for three days. I need to get out of here."

He stormed out of the med bay while the other two watched him go. Then Optimus turned his attention back to Wheeljack.

"But this problem can be corrected?"

"Easily," Wheeljack confirmed as he began typing. "I'll just need a few minutes to correct the code and she'll be good as new."

.

Later that day, Ratchet's sulking form was found loitering in Wheeljack's lab when he walked in.

"I thought I'd find you here," Wheeljack said. "Since the med bay is your usual brooding place and I figured you weren't ready to go back."

Ratchet was hunched in Wheeljack's chair, elbows on the table and fingers laced in front of his mouth which was set in a firm line. "How did it go?"

Wheeljack grabbed his extra chair and wheeled it over. "Fine. I'm letting the kid stay offline for a while longer while her system recalibrates. She could use a good rest after what she's been through."

Ratchet clenched his jaw.

"You know Wheeljack, the human medical community has a saying in one of their ancient languages: primum non nocere. It means 'first, do no harm'. I am very doubtful that we have not done any harm here. You and I may not be creatures of nature, but I know enough about it to know when I've messed with it too much. We never should have put that human into a metal body. We have tampered with something natural and now we have something very unnatural on our hands."

"It wasn't our call, Ratchet," Wheeljack countered. "We were just following orders. We weren't the ones who-"

Ratchet slapped his palm on the table top as he turned to face him. "I don't care! There should be a point where we're allowed to say no! Organic things die! They have a point in life when it's their time to go and we don't have a right to mess with it!"

He moved his hand to cover his face and his rage seemed to crumble as his voice went weak with emotion. "She tried to tell me something was wrong and I thought I knew better. I got so swept up in everything else..."

He played back all the instances in his head where he should have payed more attention. The way she moved, the way she sulked around and avoided contact. When Jazz had visited, her emotional reaction had been misinterpreted by both. She had been shaking from the pain. And what really caused the medic's spark to ache was knowing that the girl had chosen the pain of the contact rather than go without being near her friend.

What would it have been like to be in her place? All those quiet hours sitting alone in the back of the med bay. As she sat there, did she wonder if she was going to feel like that forever?

"She tried to tell me, and I didn't listen. I made her stay that way, I slowly tortured her for three days," Ratchet choked. "What am I going to do?"

Wheeljack casually stood up. "You do the same thing you always do, Ratchet. You fix it." And with that, he walked out the door.

.

Wheeljack sat himself down in front of the monitor again. Optimus Prime was still there waiting in the medical bay for him to return. Crystal's body remained on the table, lifeless, optics dark, and the Autobot leader had kept the med bay closed in the meantime.

"I guess we're doing this just you and me," Wheeljack said as his fingers flew across the keys. "But it should be alright. I think we've got the problem solved. I'm going to restart her systems."

He stood and began to unplug all the wires that had been in Crystal's chest, then pressed a few buttons before closing the chest cavity. The sound of whirring systems powered up from the body and her optics flickered on. Crystal lay there for a moment, trying to come to terms with the sensation of all thought and feeling, pretty much all life, suddenly being cut off and then turned back on again. She stared at the ceiling until Wheeljack bent over her.

"How do you feel now?"

A look of realization came over her and Crystal sat up, looking herself over. "That feels better." She gave a little laugh of relief. "That feels fantastic! You fixed it! Thank you, Wheeljack."

"Why didn't you insist we look at you earlier?" came a voice by the door.

Ratchet.

Crystal shrugged weakly. "Everyone else came in and they were hurt. So I waited for them to get help."

Ratchet moved across the room and up to her, grabbing her chin to look her in the face. Gone were all the telltales signs: the hunched posture, the uncomfortable shifting and the dreary expression. All things he should have paid attention to, but ignored.

"I'm sorry," he said lowly. "Somehow I forgot how a healthy patient was supposed to look. Next time, if I'm too stupid to listen, you harrass me until I do, understand?"

Crystal shrugged weakly. "It's okay, really. You did your best and you didn't know."

Ratchet put both hands on her shoulders and bent to meet her optics.

"I don't care how busy we are or who else we're helping. You at least let myself or Wheeljack know so we're aware of the problem. Promise me."

Crystal nodded. She had a hard enough time telling people she needed help, but she would do her best. Behind Ratchet, she saw Optimus Prime step out the door, going off to the world she had still yet to venture into. Maybe one day she would find the courage to do that as well.

Close File #001 Harm: Ratchet