A/N Please remember it is AU and won't completely follow the game in the same order, and elements will be changed. Thank you to Syn for beta'ing this.

XXXXX

Kaidan looked up as Miranda came in to check on him. "Did they do something else to me?" He asked.

"Why? What brought this on?" She hoped it was nothing to do the baby as there wasn't adequate medical equipment on board.

"I haven't had a migraine, not even a headache. I have an L2 implant, and I've always had it."

"Right, it's in the file, and I forgot to mention it, with you being a man and pregnant." She smiled as he chuckled back. There was no doubt about it; he had the sexiest voice she had ever heard.

"You're forgiven, so how about you tell me now."

"They've given you a new one. The implant you now have isn't out there; no one else has it but you. I would hold off using your biotics; it seemed you were powerful for an L2 and now who knows how powerful your abilities have become. You will probably need to do some retraining."

"I don't have the L2 anymore; I always said that I wouldn't let anyone cut into my brain. Well, I didn't let them this time."

"Kaidan you need to rest, and I need to find the best place for you to be. I have no doubt that The Illusive Man will come and look for you. Apart from using you to get Shepard to do what he want, you're also a medical miracle. You are the first born human male to be carrying a baby. I read all the reports and know how much pain they put you through; I'm surprised you're still alive. Some people just lose the will to live. I am glad that you didn't give up."

"I'm stronger than anyone thought." He paused. "I do hope I can carry it to term and have a healthy baby, through surgery. They may have changed some things about me, but I still can't give birth naturally."

"I think you and the baby are going to be fine. As much as he's become a monster you and this kid were vital to his plans. You wouldn't be here if he didn't think that you would both come out of it alive. He wouldn't take that risk, especially as Shepard and the Normandy crew would come gunning for him if either of you died. Rest now, and I'll come back and check on you soon."

"Thank you, Miranda, for everything."

She nodded and smiled at him, her mind busy as she made plans to make sure that father and child would both be safe.

XXXXX

"Admiral Hackett, there's a Miranda Lawson on the comm for you. She says it's about Major Alenko and what she has to say is for your ears only." The young private looked up at him.

With what had just happened to Earth the whereabouts of Alenko had been put on the back-burner. If someone had news about him, he wasn't going to ignore it. "I'll take it in my quarters." As soon as he got there, he opened his comm. "Ms Lawson I understand you have news of Major Alenko?"

"Not exactly news, I have him."

"You do?" His eyes narrowed suspiciously.

"I should explain some things first. Shepard would've told you about me and how I worked for Cerberus. I was in charge of the team that brought him back. After we had destroyed the Collector's home world, I saw things in a different light and couldn't be a part of that anymore."

"Very well you left them that still doesn't explain how you ended up with my missing officer?"

"I no longer have their resources, and there is someone I need to keep safe. I still have contacts, and I like to know what Cerberus is up to now. I also want to know if there is anything I can use to help me or cause them some problems, so I have a little breathing space. I found a file, and it contained details about Kaidan, Shepard talked about him a lot and the things they did to him…I couldn't leave him there."

"Is Major Alenko alright?"

"Yes, but there is something that you need to know, and he also needs a top notch doctor to look at him, maybe a couple and some specialists perhaps?"

"Why? What are you worried about telling me?" Hackett growled he'd seen soldiers who had been in explosions so their mothers wouldn't recognise them. If Alenko had been tortured he would not abandon him, no matter what state he was in now.

"After Shepard was brought back, it didn't take The Illusive Man long to realise that the Commander wouldn't follow plans he thought were wrong. The 'not changing anything about Shepard' was coming back and biting him in the ass."

Hackett laughed. "He did what he thought was right. In our case it's a good thing, he's a decent man. I guess that works against what Cerberus wanted."

"Exactly, from what I read–."

"Wait! You read you don' know?"

"I was with Shepard on the Normandy. I was to help stop the Collectors. The Illusive Man has different people running various projects. He doesn't like them to overlap in case something goes wrong, like top agents leaving."

"Very well, please carry on."

"It seemed he'd come up with a plan so that he could exert some control over Shepard. From the Intel, he'd gathered it seemed that the Shepard and Kaidan were very close." She held up her hand before he could interrupt her. "They weren't in a romantic relationship; there was nothing but a professional relationship and friendship. But it came across that the cared very much for each other."

"So The Illusive Man took Alenko so he could pressure Shepard into doing what he wanted?"

"Yes and no, just having Kaidan wasn't enough for him, he needed something more."

"What exactly is this more?" Hackett knew that this was the part that had bothered Miranda from the start and she'd had to build up to it.

"They experimented on him; put him through horrible, painful tests and procedures. That is until they finally got the result they wanted."

"Which was?" He still remembered all those men that died on Akuze for Cerberus tests. What had they done to the Major?

"He's pregnant, and it's their child, his and Shepard's."

"I'm sorry did you just say that Cerberus experimented on my officer and now they're able to impregnate men?"

"Yes, I'll send you all the files I took. I could have just hidden Kaidan away, but he needs to be checked out. I want to know that both father and child are healthy. Shepard always talked about you and Anderson how much he respected you both. I couldn't get hold of Anderson and then I found out about the attack on Earth. I don't know where to take him."

"Yes, I can see the problem. Shepard did get off Earth; he is alive and well if you could pass that onto the Major for me."

"I haven't told him that Earth was attacked."

"Ms Lawson, I think it would be better if he heard it from you and it not suddenly sprung on him wherever we put him. It will help him to know that the Commander is around. Contact me tomorrow, and I'll see if I've found out where he can go. I doubt that you would give me a way of contacting you."

"I need to have some protections. I want Kaidan to be safe, but I do have other responsibilities that are crucial."

"I'll talk to you tomorrow."

"Very well Admiral."

With that, the screen went black, and Hackett rubbed tiredly at his face. His computer beeped, and there was the file from Miranda. He would pass this onto Dr Chakwas; she knew Alenko and would be able to bring others in if needed. The Citadel could be the best place for him, but there would need to be tight security in place. He'd contact Udina and see what could be arranged. If this could be replicated how humans looked at certain things would change. Elements that were always a part of them would no longer exist.

XXXXX

"Kaidan I contacted Admiral Hackett, he's going to try and find somewhere safe for you."

"I know this is taking you away from your search to find your sister." He laughed at the look she gave him. "I overheard a conversation you had. It sounds like finding her is important and needs to be done as quickly as possible. Why don't you just put me on a planet? I'm sure I can find someone to take back to Earth. My parents must be so worried that I am missing. As soon as I get there, I'll head straight to Vancouver…what's wrong?" The sadness on her face suddenly had him terrified.

"There's something I need to tell you."

"Is John okay?"

"Hackett said he was alive; there's no easy way to say this, so…Earth has been attacked by the Reapers.

"My parents?" Kaidan whispered in horror.

"I don't know, I'm sorry. I can't get a hold of any of my contacts there. Hackett or Shepard could find out for you when you speak to them. All I know it was sudden and devastating."

He chuckled bitterly. "Not that sudden how long has Shepard been telling them about this?"

Miranda watched as he placed a hand protectively over his stomach. He turned and then walked away and back to his quarters. With all this chaos it was even harder to find out anything about Oriana. If her father or The Illusive Man had done anything to her sister, she would make them pay no matter what it took.

XXXXX

Hackett placed a hand on the wall next to the window as he stared out into space. Udina was an asshole; he'd never thought that the man would refuse to help. How dare, call the major an 'abomination', it hadn't been his fault, Kaidan was a victim. If they weren't at war and needed his connections, he would've made sure the man was out of a job. The Councillor liked the power trip a little too much.

"Sir, Asari Councillor Tevos is on the comm." A voice echoed around him.

"Put her through. What can I do for you Councillor?" He hoped that there wasn't any more trouble.

"Admiral Hackett, Councillor Udina came to us, it was about Major Alenko. He wants the young man to be taken in for 'observation'."

"I'm not going to allow that to happen."

"I agree with you, that is why I have decided to contact you. There is something that bothers me about his attitude. I will keep a closer eye on him. He seems to be outraged at how the Major has been physically altered; he acts as if this crime Councillor liked on him."

"Unfortunately even now Councillor Tevos some humans are bigots, they believe that they have the right to do so."

"We have the same problem with how some people look at a child of two Asari people; they are called 'purebloods,' and that is an insult. It was the lack of concern over the horrors that one of his people had been through. This could be a great thing for your people. I would like to offer my services."

"Your services, in what capacity?"

"Until you decide on where you're going to place him, I would like him here at the Citadel. He will, of course, be under Asari protection. Huerto Memorial will make sure that everything is okay with him and the child. I'll have commandos to protect him, and we'll restrict the people that can visit him. I am very concerned about his safety."

"Do you think Udina would do something to get Alenko out of the way?"

"If not him there are others who would like to get rid of someone who changes who they are at the most basic level. I have observed the humans for a long time, and I do believe that there are those who would feel the loss of their masculinity."

"You're not wrong Councillor and thank you. Your help in this matter would be appreciated. There is one other topic I would like to bring up, there is a woman who rescued him, and she has given us the files on not only what has been done to him, but other plans that Cerberus has been involved with. Miranda Lawson, she has left them, and she's the one that is bringing the Major here to the Citadel."

"I don't like the idea of helping anyone who worked with Cerberus, but we did with Shepard. Very well, I'll make sure that she is given a pardon by the council."

"I think Ms Lawson is planning to cause them a lot of grief. With her out there doing whatever she can to get in their way, Cerberus will be spreading themselves a little thinner." Tevos smiled and nodded; there was suddenly a black screen as she had cut the connection. At least now they had a plan, but the whole Udina conversation had him on edge. The man was a weasel, but he'd never done anything like have someone killed, well to his knowledge he hadn't. Kaidan Alenko was not going to be hurt, and it would be his choice on what to do with the child. This situation was forced onto him. The only person he needed to talk to was Shepard. Hackett couldn't help but chuckle at a little mini Shepard or Alenko running around. He'd bet that kid would be as stubborn as anything; it was also going to be the cutest and most spoiled child ever born.

XXXXX

Udina glared at the message that confirmed one Kaidan Alenko would arrive at the Citadel as a guest of the Asari. There were a few reasons that he didn't want this 'man' if he could still be called that. The Major was now a freak of nature, an embarrassment to the human race. He'd thought at one point to promote him to the second human SPECTRE; he was glad that this happened now. What would the others think of them, of him if this ever got out? The other problem was Cerberus, they were going to take over the Citadel, and The Illusive Man seemed obsessed about getting Alenko back, some commandos protected him. At some point, Shepard was bound to turn up. Udina hoped it would be after the coup. It was a damn shame that he and Anderson hadn't died when Earth was attacked. A dead Shepard, a dead one would've made him a martyr, and that was something he could have used.

XXXXX

"Kaidan, everything has been arranged. We're going to the Citadel; you're a guest of the Asari. It sounded like Udina didn't take the news of your pregnancy too well. There are concerns for your safety, so you will be guarded and have a very restrict visitors list, which all will be vetted."

"What about you Miranda, will they take you into custody?" The two of them had become close, and he would do anything to make sure she was free to look for her sister.

"You don't need to worry Admiral Hackett has sorted it out. I think they like the idea of me out the causing problems for Cerberus." She laughed at the thought of all the things she could do.

"Does Shepard know about me, about this yet?" He waved his hand slightly bulged stomach.

"Not yet, Hackett's going to tell him when they next debrief."

"I hope he's sitting down when he finds out; I'm not sure it will be good for his rep if the saviour of the Citadel fainted." He had this fear that the man he cared for would turn from him or even hate him because of what had happened.

"Shepard's a good guy. It was also clear when he mentioned you how much he cared. You could hear it in his voice, see it in his smile. It only happened when the conversation turned to Kaidan Alenko."

Kaidan lowered his head, bit his lip shyly, but a sweet smile appeared on his face.

XXXXX

"Admiral, did you get the files about the Prothean device from Liara?"

"Yes I did Commander; I already have people looking at it." Hackett paused for a moment. "There is something you need to know."

"What is it? Have Cerberus caused more problems?"

"I guess you could say they have. I need to explain a few things, and you aren't going to like it."

"Okay." He already didn't like the way this sounded.

"Anderson kept up to date about you asking for anything about Major Alenko, wait until I've finished. You're going to need to hear all of this." He waited until Shepard nodded in agreement. "The reason you weren't told anything was that at the time we didn't know where he was." He could see the other man's jaw clench, his hands made into fists and then relaxed. "He was supposed to be on Horizon; he should have been there when you arrived. He was intercepted on his way there. Until recently, very recently we had no idea what had happened to him. I was contacted not long ago by an acquaintance of yours, Ms Miranda Lawson. It seems that she was digging up information for another reason and found out about Kaidan. She knew that the two of you were friends, so she rescued him. But it wasn't soon enough, the next part is going to be hard to believe, but the medical data doesn't lie, and if they managed to bring you back from the dead. Well, anything is possible with Cerberus. Just remember none of this is your fault either, it's all on The Illusive Man."

"Please just tell me what they did to Kaidan, and when can I see him?"

"When you were brought back it seemed The Illusive Man didn't quite understand the kind of man you were. You weren't going to follow him blindly. He knew that some insurance to make sure you did what he wanted when he wanted. His informants told him that you and Kaidan were close if you hadn't been in the military that you would have been together, in a romantic relationship." Hackett clarified. "The thing was that wasn't enough for him. From what Miranda said and the doctors, he was put through a lot of painful tests and experiments until he got the outcome that he wanted. Commander, the Major, is pregnant with your child."

Shepard opened and closed his mouth a few times. He'd planned what he was going to say, but now his mind was blank. "Kaidan's pregnant?"

"Yes he is, and he's currently on his way to the Citadel. The Asari have him as their guest and under protection."

"Why them and not us?"

"Udina hasn't been supportive about this. There are concerns he might try and do something to make this 'embarrassment' disappear."

"Kaidan and our child is not an embarrassment," Shepard shouted automatically.

Hackett smiled at him. "It's good to hear you say that. He's going to need a lot of support especially from you."

"What about Miranda?"

"For all of her help with you and the Collectors and for rescuing one of our officers, she's not going to be arrested. Councillor Tevos is going to make sure she has a pardon for past Cerberus activities.

"We're going to be fathers." He muttered with a dopey grin.

"Yes Commander you both are. You're going to need to talk to him and figure out what you're going to do next. Until you decide, I think it's best that you tell no one. We don't want anyone to go after them."

"I'm sure I have enemies that would be more than happy to cause me pain by going through him." He took some deep breaths as soon as he felt panic come on.

"Contact me as soon as you two have made a decision."

"Yes, sir."

XXXXX

Udina glanced over at the clock. It should all be over soon. Alenko would be sacrificed for the greater good. The Galaxy needed a change the Asari, Taurians and Salarians had been in charge for far too long. Once the humans were in charge, it would be a better place. Cerberus would help him get there after all their motto was 'humans first' and he supported that. All the experiments, the casualties, to him that was acceptable, it would propel them into the future they deserved. They were going to make sure that they were safe from the alien menace, any alien menace.

Just then his computer beeped, and he breathed a sigh of relief that monster was no longer going to be born. He noticed that it was from Bailey and not one of his men and as soon as he opened the smile left his face. The mercenaries he had sent had failed. Some terminally ill Drell patient who happened to be getting his treatment got involved and saved the day as he took out the leader. The Asari commandos cleaned up the others.

There was another beep as mail appeared and Udina winced. It was from Cerberus. He'd gone against The Illusive Man and was not happy that Alenko was almost killed.

XXXXX

The Illusive Man took a long drag from his cigarette and turned to Kai Lang.

"If Udina ignores my orders again, please take him out and when you are on the Citadel send him a clear warning that this will not be tolerated. If he wants to be a part of the incredible future that humanity is going to have he needs to step back in line."

"It will be my pleasure, what about Shepard and Alenko?"

"I want them both alive unless they get in the way and you have no other choice. If that happens to deal with them as you see fit."

XXXXX

A nurse checked over her patient. She was thrilled to be part of this case and was honoured to be asked. The first human born male to be pregnant. She frowned as she noticed something.

"Are you hurt?"

"No, I'm fine."

"Are you sure?" She asked.

Kaidan looked over at her with concern. "Why?"

"There's some blood on your dog tags."

"Oh,' he breathed a little easier. "It's not mine; it belongs to the person who took me." He never understood why the reclusive leader of Cerberus came to see him. "Can you do every test you can think of on this blood and send it to Admiral Hackett?"

"Okay." If this would help catch the people that kidnapped people to experiment on them, then she would do everything she could to help.

XXXXX

Admiral Hackett couldn't believe what he as reading. He'd been told about the blood and who it belonged to. Any extra information on that man would be gratefully received, but he never in his wildest dreams expected this. The Illusive Man was Commander John Shepard's biological father.

TBC