Just a quick part added before I take a much needed break for Christmas.

Hypn0s : That's one game I've actually never played so I'll take your word for it. I got most of my inspiration from Dr Who, Resistance: Fall of Man and Wolfenstein's Uber Soldats amongst others.

Obsessed sniper: I'm definitely planning a battle royale Hoover Dam style and hope I can meet your expectations.

Geraldford: Don't worry it will be Alpha vs. Omega before long!

MrUnclePeanuts: It strikes me you're taking this a little too seriously. I try to be as realistic as possible but I've got to bring some game elements in or it wouldn't be too relevant would it? If the LW can adapt quickly why can't another vault dweller, especially one fighting for one she loves. Some people just sink, others can swim. As for the Sarah bashing (again) whoever said I was trying to justify her character? That's just how she is to me. She doesn't train recruits (that's Gunny's job), she trains elites and such considerations wouldn't cross her mind (She even thinks the LW a 'trashy wastelander' when they first meet), it's just (somewhat arrogant) Brotherhood thinking and you'll have to direct your complaining to Bethesda about that.

Jake: Glad the fic is still believable for some; thanks for that.

Alavon: I've been called a few names but never that one before. To say thanks I'll leave you with another cliffhanger! Hehehe…

Merry Christmas to all and I'll get the next part out in the New Year.

Baltimore Haven

Jim Lawson got one hell of a shock when he went out to meet his daughter home. Overcome with relief that she'd been freed and was coming back unharmed he'd run up to the Vertibird and pulled down the ramp...

"CLOSE THE FUCKING DOOR!"
Jake's angry voice and one short look inside were worth a thousand words. No one had warned him about their lack of clothing! He had to wait five more minutes, a little red faced, before three spare vault jumpsuits could be brought up.

Vault 99 surgery

Doc Farnsworth stared in heartfelt worry at his patient. Leon was curled up on the surgery bed almost into a foetal ball. He'd been in that position ever since he'd stopped freaking out on the Vertibird; he'd hardly even twitched when Dan and the other troopers had lifted him off the Vertibird and into the Vault. Frankly Farnsworth had preferred the screaming; at least it showed he was still alive and conscious. This silence worried him in more ways than one.

He saw Amata, Sarah and all the others arriving in the corridor outside and quickly moved outside to head them off. He didn't want any undue pressure on Leon at this point.

"Oh god no!" Amata was in anguish at seeing Leon through the window. Sarah and the rest couldn't believe the sight either.

"How bad is it, Doc?" Dan finally got the courage to ask.

"Very. The arms and legs are permanent; obviously. They're solid Adamantium believe it or not and mixed with some new alloy that I've never seen before. Makes it more lightweight yet even more resilient."

"What else?" Sarah knew there had to be more. Kayla, Yuna and Jake looked on the verge of throwing up knowing that could easily have been them lying there if they'd stayed in Alpha's hands any longer.

"He's also had heavy surgery. What's left of his skeleton and his skull has been Adamantium coated. His eyes have been removed and replaced by cybernetic ones that can see in several spectrums and he's had a series of new implants put inside of him. Very advanced too, I'd say they were new prototypes."
That caused Houser even more concern. "Prototypes? What kind?"

"A more advanced sub-dermal armour for one, strength and endurance enhancers that boost well beyond the normal sort and as to his immune system and healing; well it's nothing short of spectacular. Toxins and poison are now absolutely useless. It even rejected my sedative on the flight back!"

"This is altogether different from anything we've seen before," Sarah mused. "They used him as a guinea pig, didn't they?"

Farnsworth nodded. "I'm afraid so. I don't pretend to be any military expert but I would say he was designed for infiltration purposes. I've run a few simulations through the computer. His arms and legs could be recovered with flesh and skin and would look perfectly normal again. His eyes could also be touched up or simply covered by contact lenses or sunglasses. Unless you did a full scan like I just have you would never tell that his arms were metal with hydraulic muscles or ever find his other enhancements. He would look like a normal, but strong, human being."

"Those cunning bastards," Sarah was disgusted and grudgingly impressed at the same time. "This was designed specifically for Leon. Alpha gave him an upgrade that would play to his strengths; he's always been good at infiltration and sneak attacks."

"And think of what else they could do with this," Severance was horrified at the bigger picture. "An army of cyborgs that could walk among us and we'd never even know it!"

"That's not all they could do," Farnsworth went on. "Whatever else we might think of this Alpha the one thing we can never accuse him of is not thinking ahead."

"What's that supposed to mean?" Kayla asked with raised eyebrows.

Farnsworth suddenly looked very uncomfortable. "I suppose there's no delicate way to put this except to say that he can still 'organically function'."
"Oh!" Dan was the first to see where he was going though the others were still lost.

"He can still eat and still has to sleep, though he probably needs a lot less than he used to," Farnsworth explained. "And he can still procreate."

Everyone's head whipped around in shock. "You're kidding!" Severance was the first to blurt out.

Farnsworth shrugged. "I never kid about my work. The only things they cut off were his arms and legs. His um...'external plumbing' shall we say is still intact and functional along with his digestive system and all other main organs."
Houser nodded in understanding. "It makes sense. Alpha must have known he couldn't sustain his numbers by taking and converting people so he comes up with a model that can get round the problem."
"Kind of hard to get it on with a girl when you're an unthinking drone and jammed into a metal cage of cybernetic armour," Dan agreed.

"Will you stop screwing around!" Amata snapped. "This is my friend we're talking about here!"

"Bottom line: how is he doing overall?" Sarah typically cut to the chase.

"Physically he's fine. No complications or side effects, if anything he's stronger and more resilient than ever. It's his mental state that worries me. He flipped out on the Vertibird when he realised what exactly had been done to him and my concern is that he might not see himself as human anymore despite my attempts to assure him otherwise. You pulled the plug on this just in time I think. They completed the physical part of the upgrade and if they'd gone any further they'd have started operating on his mind."
"Yeah they almost did," Dan recalled with a chill as he remembered pulling Leon off the operating table. "They almost stuck a neural probe in his head."
"Which undoubtedly was a brainwashing probe," Farnsworth reasoned. "If that had gone into him he'd be just like those other primary cyborgs you encountered and irretrievable. Now if you don't mind I should get back to my patient. Amata can stay if she wants to. In fact I'd like a word with her in private."

Farnsworth led Amata through to his private office in the back of his clinic.

"If anyone can help Leon get through this intact it would be you," Farnsworth was blunt. "My fear is he'll try and handle this on his own like he's so used to doing but that could cause him to withdraw into himself and cut us off completely."
Amata shared that worry. Leon had never been one to share his inner emotions or his problems in the past and she wasn't confident of bringing them out now, but she'd never given up on a friend and she certainly wasn't going to give up on the one she'd come to love.

"What can I do, besides being there for him that is?"

"Just that; be there for him and make sure he knows that you're there for him," Farnsworth advised. "I know it sounds pathetic but things like that can be the difference between make or break."

Amata nodded. "Can I stay the night then?"

"Sure but I wouldn't get as intimate as you got last time," Farnsworth allowed himself a little smile. "At least not until he can gauge his new strength and arms. If he got too enthusiastic he could accidentally break your back."

"He's THAT strong now?" Amata was aghast.

"With those arms he is. Adamantium is practically unbreakable and coupled with hydraulic muscles...he could crush every bone in our hands down to powder."

"Right," Amata sighed. That was one way of comforting him gone to start with.

"Don't fret; he's strong and the parts that make us truly human, the heart, mind and soul, are all still exactly as they were. Never doubt that. Just try not to get too shocked by his new eyes, they are...different."

Amata nodded in understanding and took a deep breath. No point in putting it off any longer I suppose.

She approached his sleeping form with heavy trepidation. She blushed as she gazed at his improved muscles, he'd been pretty buff before but now he was even more developed, you could tell even through the undershirt he'd been given to cover his dignity.

"Who is it?"
Amata was jerked back to reality by his voice as he awoke and sat up on the gurney. She sucked in a breath as she saw his new eyes; Farnsworth had been right, they were unsettling, like a cross between a cat and a demon's.

Leon sighed as he saw Amata and her reaction and looked away from her. His eyes freaked him out never mind her. "Amata...I didn't think you'd want to see me like this."
She could see the hurt he was feeling. "Leon, I'm so sorry."

"Don't be. It isn't your fault. I screwed up back there not you. Besides what would your dad have said if you'd come back looking like this?"

"Oh Leon, always trying to protect me," Amata sighed. "I wish you'd let me help more once in a while. We could have pulled you out..."

"Not in time. We both know that," Leon wasn't in the mood to debate this. "But from what the doc told me you were the hero this time, pulling the plug on the vault's power. Thank you for that Amata. As bad as this is, at least I didn't get turned all the way."

"Does it hurt?" Amata asked with real worry.

"No it doesn't. What's scary is I can't feel anything through them at all. I mean these things are attached to me and they work but I can't feel them anymore...god what am I now?"

"You're still you," Amata could feel his pain. "They may have violated your body but they didn't touch you inside."

"Really?" Leon scoffed. "From what I've been told there's more spare parts in me now than a junkyard; plus every time I look in a mirror there's these staring back at me! Shit, I can't even cry anymore!"

"You're still the same person inside that I knew," Amata plucked up all her courage. "And you're still the only man in this world I love."

Leon was beyond stunned. I knew she liked me before but she didn't just say that now, did she?

Thirty seconds later he found his voice again. "I look like I've had an accident with a trash compactor and you're saying...?"
Amata couldn't hold herself back anymore as she flung her arms around him and kissed him. For the second time in a minute Leon was taken aback and it took ten seconds before he responded and could gently return her kiss.

"You believe me now?" Amata said as she broke away. "It wasn't just your looks I fell in love with. It was the man inside, the same one who looked out for me growing up in the vault. You're not alone in this, Leon, and you're still human no matter what anyone else says. I believe in you, the question is: do you?"

Leon couldn't help smiling for the first time since his conversion. "Touché. I suppose I was asking for that, wasn't I?"
Amata broke into a smile. "Forgetting your own lessons. Slipping aren't we?"

Leon held up his arms in response. "Seriously though, am I really what you want now? This could be difficult unless you're into heavy metal..."
Amata choked back a laugh. "The doc says that can be fixed, same with your eyes, and it's pretty light metal from what I hear."

"Maybe but I need to get used to these first. If I get...too excited, I could really hurt you. I could never forgive myself if that happened."

Amata had to admit he had a point there. "We'll work something out, don't worry. I love you, Leon, and your condition will never change that."

Leon was touched beyond words. "I love you too. Hell I've loved you for years but I could never bring myself to say it."

Amata knew that feeling all too well. If only she'd not been so short-sighted the year before...

"Well congratulations are in order then." Doc Farnsworth had quietly come out of his office and had caught the last parts. "You managed to perk up my patient much more than I ever could and you two are together now."

"Thanks, Doc," Leon managed after he and Amata broke apart in embarrassment.

"I came to tell you we're getting some more armour and food sent up for you. I bet you're hungry by now."
"Starving," Leon agreed.

"I'd still like to run a few more tests and perhaps look through your pip-boy. The other cyborgs had detailed schematics of themselves in theirs and yours might offer some insight too."

"I'll catch up with you later," Amata beamed as she left feeling better than she had in awhile. Her relationship with Leon was on better ground than she'd ever thought possible a week or so back. Still there were now some new problems to get around as she headed for the cafeteria deep in thought...

Vault Cafeteria

"You ok?" Sarah asked Amata who was still deep in thought.

"Yeah, I'm fine. Leon's getting better and so am I. How are the others?"

"Kayla's back on her feet and getting debriefed with Dan. Jake and Yuna are getting some much needed rest. I think those two are getting closer if you know what I mean!"

"So are Leon and me," Amata revealed. "It's just with him being half metal and me not..."
"Damn," Sarah didn't know what to say to that. "I just hope you two can get around that somehow. Anyway, to change the topic completely, this might not mean much to you right now but I'm putting you in for Knight when we get back."

"You're serious?" It was Amata's turn to be stunned.

"Absolutely. I know your name hasn't even been added to the scrolls yet but I'm confident my father and Rothchild will agree on this. You were the keystone in the last mission, sneaking into the heart of an enemy stronghold and saving a Knight Commander in the process. I don't think Leon can argue much against this now. You're better than most wasteland recruits we get and more than good enough for a full Knight. I'd love to know what makes you vault dwellers so damn tough!"

That makes two of us! "Thanks Sarah. Coming from you that means a lot. In fact, that's just given me an idea. I've got to go see the doc."
She headed for the infirmary leaving her meal half eaten and a puzzled Sarah behind.

Vault 99 surgery

Amata returned to find Leon already gone.

"He left half an hour ago," Farnsworth came out of his office to meet her. "Said he had some new plans for those arms of his and left for the armoury to find Matt and Mira as soon as his replacement armour arrived."

"That's ok. It wasn't him I was trying to find. I need a favour, doc."

"What kind? You don't look wounded or very ill so I can assume it's not treatment you're looking for."
Amata looked awkward. "In a way it is. I was wondering: does this vault have any Adamantium?"

"Sure it does. We, the Enclave that is, have a good stock of it as well. Used in both armour and construction work mostly, why?"

Farnsworth's eyes grew to the size of dinner plates when Amata explained what she had in mind.

"You can't be serious!" When Amata's deadly serious expression didn't change he knew that was a wish too far. "Oh dear lord, you are. This isn't risk free you know. Reading it from a template is one thing, actually doing it is quite another."

Amata's voice took on a pleading tone. "I know. But I don't know any other way. I don't want to beg but please. I need to do this. It's not just me being selfish. I failed Leon last year. I sent him out of the vault when he needed my help most and look what happened. If I'm to stay with him I need to get stronger and tougher."

"As laudable as that is you put me in a difficult position," Farnsworth fretted. "I'm sworn to do no harm as a doctor and this could kill you if it goes wrong."
"Yes I already figured that out. But unless I do it I don't think I can ever keep up with Leon or...well you know. You made that perfectly clear."

"Yes I did," Farnsworth admitted he'd run himself into a corner on this one."If you won't be persuaded...go and lie on the table over there, once you've stripped down of course."

Armoury

"Is this everything you need?"

Matt and Mira had spent the last half hour getting Leon a long list of equipment and spare parts. It was an odd list as far as they could see. Several suits of leather armour, a few Chinese swords, an acetylene torch, an arc welder, a sledgehammer and access to a workbench and other various tools.

"Yeah that's fine, thanks for all this. I can take it from here."

"What do you need all this for?" Mira couldn't see the need for leather armour when Leon was wearing a perfectly good suit of Combat Armour.

"If I'm stuck with these arms I might as well improve on them a little. If other cyborgs can put weapons on their arms so can I."
Matt nodded. "Ok, if you need anything else..."

"You'll be the first guys I call. Thanks."

Amata had managed to pull Leon from his depression but his feelings of hate were going into overdrive as he started to work. You made a fatal mistake doing this to me and stealing my humanity, Alpha. I hope you're ready for some serious consequences...

Vault 66

"No...NO...AAAAAAGGGGGGGGGGHHHH!"
The scream would have curdled the blood of any human who would have heard it. In the aftermath of the Enclave rescue Alpha, Delta and Iota had been moved to a hidden area below level 5 that served as the cyborgs' healing and 'regeneration' area. This was one of the most gruesome areas of the whole vault, more so than even the upgrade chambers, as this was the place where unfortunate wastelanders were taken after capture, forced into big Auto-Doc style cylinders and then chopped up for 'spare organic parts'. The saws and cutters literally dismembered the poor victims then their flesh was liquefied and sent to the giant vats for reprocessing and distribution to the transparent glass healing chambers above.

Delta and Iota had just finished their healing cycle and were emerging from their pods fully restored. Their flesh had been badly burnt by Severance's grenade shot but now it was as if it had never happened. Both watched the disgusting sight of Alpha's wounds fast healing as fresh blood, flesh and skin poured through pipes into the chamber. Five minutes later he emerged fully restored as well and in less than a good mood.

"Give me a full damage report!"
"We have lost 50% of our drone upgrade capacity," Delta knew this was going to be a sorry report. "The primary chamber has been badly damaged also and is undergoing repair. All the captives eluded us...including unit Omega. The computers report his upgrade was incomplete."

Alpha knew that much already. He'd been about to complete it when the power had been cut. Once again history repeats! Those pre-war government filth are ruining everything I've worked to accomplish!

"Repairs to the primary chamber will take hours at least. The grenade caused extensive damage and it will take our drones a lot of time even with full vault power it still needs..."

"It will take longer because I have another agenda in mind," Alpha cut Delta off abruptly.

"And that is?" Delta saw the growing rage in Alpha's words.

"Reactivating all units from storage chambers A and B and sending them against Baltimore Haven!"

Even Delta was taken aback at this. "Reactivate all of them? At the same time?"

"Correct. Omega is a vital part of our future and development. His recovery is imperative at all and any cost."
"And what of the settlement itself?" Delta asked.

"Preserve what you can of it and bring back as many prisoners as possible from the settlers to replace the units we have lost. As for the Enclave..." he spat that word with utter hatred. "They have defied me, no us, once too often. Delete every single one of them!"
"Gladly," Delta broke into a chilling smile of his own. Deleting 'organics' was a cherished pastime of his.

"We will need at least a day and most of the vault's power to reactivate all the units required," Iota warned.

"Well then I suggest you begin immediately! Start by bringing Sub-Commander Theta online to lead alongside you and then make sure that all the heavy cyber suits are ready for battle as well. I want that settlement taken and Omega recovered by the end of the week!"

"Complying!"

Delta and Iota hurriedly left the room and went down an access corridor to another vast chamber. This one had glowing blue glass pods stacked high as far as the eye could see. If Leon had been there he'd have recognised them at once as Zeta alien cryogenic technology. Though he wasn't aware of their origins Alpha had been able to reverse engineer and replicate them quite easily. He'd upgraded hundreds of people over the years and then, to save on space and resources, had put them on ice in the chambers. A fully capable army ready to be released at anytime...and that time was now. Delta tapped the reactivation sequence into the nearby console and watched as power and heat was applied to each pod and the cyborg occupants began to thaw and reanimate.

Delta and Iota shared a cold smile. Now they numbered a few dozen. In a day there would be hundreds of them and Baltimore Haven would learn what defying the cyborg race would really mean. It would be a glorious battle and the start of a new cyber era...