AN: Okay so this is the story that has been eating away at me for months on end as I tried to figure out how just to go about actually writing it. Finally I have come to a decision about the way to go about it. So I can start.

I hope to keep this updated as regularly as I can, as for the moment it will follow the plot of ME2 and into ME3 though dialogue, order and possibly some events may be changed to better suit the story that I am trying to tell.

Oh and this was inspired by "The mission stays the same" an amazingly well written MEx40K crossover that I would recommend to anyone who is into the idea of these two worlds being crossed, and it is ultimately much better than anything I could ever hope to write.

Having said that I do hope you enjoy my story. The first chapter is ME setup, the second will be 40K setup and the third will be the start of the crossover, you will also probably see the chapter length increase at that point as well.


Normandy SR-2, Undisclosed location


The airlock of the Normandy opened to reveal its, up until recently deceased, Captain. Commander Lillian Shepard, she was still wearing her hard suit from the mission on Freedoms Progress, electing not to remove it whilst still wandering around a Cerberus base. She knew that it seemed rather idiotic to place such little trust in those who had just spent two whole years and god knows how many credits to piece her back together. Yet she could not shake of a feeling that she had about the organisation. She remembered the experiments they had uncovered two years ago when chasing Saren, she recalled the callous nature the Cerberus scientists were willing to throw aside their humanity as long as it got results. It was this very lack of humanity that Lillian could not understand, no matter how hard she tried. To some point she was very good at seeing the other point of view, something her mother had taught her at a young age was to understand the other side. This was why she could understand why people supported the ideals of groups like Cerberus and Terra Firma. She personally did not agree with them, but she could understand why some people could feel they way they do.

After all it had been less than three decades since first contact. A first contact that had not been the most peaceful of scenarios, and it had quickly highlighted to many people that humanity was not only not alone in the universe but this galaxy alone was full of threats to the sovereignty of the people of Earth. Almost overnight organisations such as Terra Firma had seemingly appeared out of the civilian population, many of the immediate backers were friends, families and even some soldiers who had lost people at Shanxi. An understandable knee-jerk response in Lillian's opinion, not that she had been old enough to have an opinion at the time. At the wise old age of three, the first contact war passed the youngest Shepard by without even a question being raised, and it would not be until she was much older that her mother sat her down and explained what had truly happened, not the stories that were spread around like propaganda, but the truth as she had seen it as an officer serving at the time. Her Father however never spoke of his experiences on the ground. Shepard never asked either. As a child she had asked questions and he would simply make up stories, but as she got older he became quieter and quieter on the subject, and the stories disappeared. Now a soldier herself, Lillian understood why her Father did not wish to expose his daughter to such things.

"Commander?" Came the enquiringly voice of the ship's XO, Miranda Lawson. Who was wearing what Lillian would describe as highly inappropriate attire for the crew of a starship, but it was quite possible that Cerberus worked with different regulations. "Are you alright?"

Lillian could tell that the falsified tones of concern were simply an act, Lawson was more concerned that the Lillian's cybernetics were being rejected, something she would consider a personal failure. Lillian had not known the woman for over three days, but it was already very clear what type of person she was. It was clear from the way that the woman held herself that she had great confidence in not only her abilities but also her figure. Which annoyingly Lillian could not argue, Miranda had an amazing body structure, if Lillian was unaware of the process of evolution she would have believed that Miranda was gifted by the gods, she looked almost designed.

"Just lost in thought Miranda." Lillian responded in her usual no nonsense tone. She didn't like having to act like a drill sergeant, but around these Cerberus operatives it seemed like the best idea.

"If that is all Commander please follow me." Miranda did not even wait for a response from Lillian and started to make her way into the ship and on to the CIC.

The CIC of the SR-2 was much like its predecessor only much larger in scale. The Galaxy map sat to the rear of the area with a holographic image of the ship itself present in over the forward region of the consoles. Lillian walked over to the console and for the first time studied the ship's specifications. Certain things had been clear from the outside such as the SR-2 being almost double the size of the original, not to mention the basic difference in appearance. Here however the specifications of the ship were listed, its total mass, armaments, crew compliment, cargo capacity and there were even details relating to the drive core and the stealth systems which had also been improved over the originals.

"She does seem impressive." Lillian said before Miranda could ask her if she was alright again.

"I am glad you agree, we spent over two years building her." Jacob Taylor was the person who answered her this time. "Made some seamless improvements in the process, the old girl was a prototype. Now she is true and tested."

In contrast to Miranda, Lillian liked Jacob. He was more like her, a Soldier. He was straight forward with his opinions and had made it very clear from the beginning that, whilst he did work for Cerberus, he did not trust The Illusive Man nor did he agree with many of the methods that the organisation had employed over the years. He had also been very clear that he was proud however of the work that he had done with Cerberus over his tenure. He even told Lillian about the time him and Miranda had stopped a Batarian attack on the Citadel. Something she had thanked him for since no one else had even taken notice, not even Miranda and she had been there.

"It is not the same, though you probably already worked that out just by looking at her," He continued on informing her about some of the background to the ship she was currently standing in. "The power systems and stealth systems have been overhauled with the latest technology and an extra deck for crew cabins was added. There are quite a few spare since the ship is quite capable at operating on a skeleton crew."

"But you didn't improve the weapon system or the armour?" Lillian commented as she continued to overlook the specifications. "Trust me, I was there last time. If we don't upgrade those systems we don't stand a chance against the Collectors."

"The Normandy was built to the original specification unless specified differently by The Illusive Man himself." A synthetic voice rang out over the CIC before a hologram appeared in front of Lillian. "Welcome Commander Shepard."

If she was honest this was not what she had been expecting. A crew of talented xenophobic individuals, whilst still a possibility, was currently looking less likely judging by the reactions of both Jacob and Miranda to the Quarians they had bumped into of Freedoms Progress. Neither of the two Cerberus operatives had seem phased in the slightest by the Quarians, and when spoken to they had replied how you would expect anyone to reply. Something that Lillian had been extremely grateful for since it had made securing Tali's help much easier. If anything the problem had been from the Quarians side, Prazza had been unwilling to work with Cerberus and had paid for his decision with his life, much to Lillian's regret. However an AI was not something she had been expecting from Cerberus, though now that she actually gave it some thought it did seem to fit their modus operandi of taking high risks with experiments that were usually against Galactic law.

"I wasn't expecting an AI on the ship," Lillian commented, keeping her internal musings about Cerberus' modis operandi to herself. "What do we call you and what do you do on-board the Ship? Since we have Joker I assume you don't pilot it."

"I am the Normandy's Enhanced Defense Intelligence, though most of the crew refer to me as EDI." EDI responded, the slight artificial emotion in her voice playing through. "And you are quite correct commander, Mr. Moreau's talents will not go to waste. I am simply here to offer tactical and scientifically analysis and insight. In combat I control the Cyber warfare suite."

"Glad to have you on the team." Lillian ended that conversation there, though she made a mental note to get to know EDI better later, when she was not surrounded by Cerberus operatives. "Alright, dismissed I will come and find you before we are ready to depart."

Miranda and Jacob looked at each other slightly confused.

"Shouldn't we at least give you a run-down of the basic features and changes we have made to the Normandy?" Miranda asked, as though she had been waiting for this part since they stepped onto the ship.

"Miranda I will have a look around for myself, meet with some of the crew and learn about the ship on my own. It is the best way." Lillian replied, with a smirk on her face. For some bizarre reason she was taking too much pleasure in denying the Cerberus operative the joy of showing her around. "I will find you and then we can discuss our first course of action once I have finished my tour."

"As you wish Commander." Lillian was not the only one who caught the sneer in Miranda's voice, judging by his facial expression Jacob also picked up on it.

However without another word Miranda simply walked on by the two of them and over to the elevator at the back of the CIC and stepped in. She was most likely going to her own personalized office, Lillian assumed, she was the type after all.

"Well speak to you later Commander." Jacob said to her, obviously not as bothered by not giving the tour as Miranda was. "I'll be in the armoury if you want to talk."

With that Jacob left, though he did not head to the elevator like Lillian expected, instead he headed through the door on the far right of the CIC. For a moment Lillian stood in the middle of the CIC rather stunned, wondering what idiot in their right mind decided that the CIC was a good place for the armoury. It was something that she was going to have to discuss with Miranda and Jacob and see about getting it moved, most likely down into the Cargo hold like on the original Normandy.

However that was not the first issue that was on Lillian's growing agenda. The first thing she did was head for the elevator and up to her private cabin, one of the few things on the new Normandy that she was aware of due to a quick discussion with Joker earlier in the day that had revolved around some of the new features. The pilot had been more interested in the new leather seats than he had in her private living quarters, something that she was rather thankful for if she was completely honest with herself. The last thing she needed was Joker jealous of her living quarters. But she didn't have much to worry about apparently Jokers own quarters on the new deck, whilst nowhere near as large as the private captain's cabin were apparently "substantial" even to his extreme standards.

She allowed herself a small silent laugh as she stepped out onto the small landing in front of the cabin as she thought about Joker with a small collection of model starships hanging from his ceiling like a hyperactive child with a love of starships. In many ways that was the way that she viewed Joker, he had always come through when he needed to and he could be surprisingly astute with his observations. Yet the Pilot did well in living up to his flight school gained nickname, always hiding his true feelings behind a layer of dry and often rather poor attempts at humour.

Lillian's mind was instantly removed from thinking about her pilot as the door opened and revealed her living quarters. It was a very large spacious area, especially on something as constricted for space like a starship. The main area was divided into two sections, one was designed as a bedroom like area, featuring her bed and a seating area for guests. Not that it was ever likely that she would be entertaining guests but it was nice to know she could if the need ever arose. The locker for her armour was also located in this area. The second area which sat on a slightly raised platform and was the first thing that anyone walking into the cabin would be greeted with was an office like area with a desk sitting on the right that overlooked the rest of the cabin through a glass display case. On her left was what looked like a fish tank, though there were currently no fish in the tank itself. Lillian thought that was probably for the best, she would never have any time to look after any sort of pet, even something as simple as a fish.

Silently she decided that she would have an explore around the cabin later when she had some free time, but at this exact moment the only thing that she really wanted to do was get out of her armour that was slowly becoming heavier and heavier as she realised just how tired she was. Really it was not that surprising that she was feeling so wore out, she had not slept since she had been 'resurrected' and in some ways she feared closing her eyes with the terrifying thoughts that she might never wake again. It was not something that she could hide from herself or that she could run away from forever, but she was definitely going to try and avoid it for the next few hours.

With practiced skill she undid the clips that held her hard suit in place, allowing the plates to fall gently to the floor leaving her in nothing but the skin tight under suit. Calmly she tidied the plates away, neatly packing them into the armour locker after checking each and every one of them for marks and damage. It was something that her N7 drill instructor had ironically drilled into all of his students. Armour maintenance was one of the key features that many marines choose to side step, feeling that it was too time consuming and any real damage would be detected by the ship, base or facilities quartermaster. However this was not the case for the N7 candidates. N7 operatives were expected to maintain their own equipment to the standard of an armoury officer, of course this meant that Lillian did not have to rely on Jacob to fix her armour should it become damaged, though she would probably allow him to carry out most maintenance just to so that he could keep on top of the resources used more than anything else. Once her armour was checked and cleared of any faults she finished packing it away and professionally removed the skin tight under suit. The material that the under suit was made from made it harder to remove than most people believed, as it would stick to the skin and result in turning itself inside out when removed. However the material was made so that it could be worn either way with minimal irritation to the skin, so it was not a major concern for any soldier.

All her armour cleared away she looked quickly into the wardrobe that was already in the room and stocked with standard Cerberus uniforms for her to change into. She chose the one that most of the crew seemed to be wearing, but she was going to be talking to Miranda about the clothing options as soon as she was able, and let herself appointed XO know that the Cerberus motifs and symbols were going to have to be removed from the entire ship. After all Lillian knew of the reputation that Cerberus had and she was only going to be hindered in anything she tried to do by flying that flag.

Without warning EDI's hologram appeared near the door.

"Commander, Mr Moreau is requesting that you come and speak with him before you decide on our first destination." EDI informed Lillian of her pilots request.

"Thank you EDI, I will add it to my list of things to do." Lillian informed EDI as she finished changing. "But I am going to tour the ship first and get to know some of the crew, so let Joker know it could be a few hours before I get round to him."

"Understood Commander, logging you out." With that EDI's hologram disappeared leaving Lillian on her own again.

She let out a rather large sigh and then silently made her way back to the elevator deciding to start with the most comfortable place on the ship to her, Engineering.

The door opened to the engineering deck, revealing a long corridor with windows that ran most of the length looking out on to the main cargo deck of the Normandy. Lillian could see that it was much like the original Normandy in the way it was laid out with the exception that there was no Mako, nor was there any armour lockers. However what there was docked in the cargo bay were several small shuttles. She had managed to look over some of the changes that had been applied in the two years since she had 'died' and these Kodiak's were now widely used. Not just by the alliance and other human organisations but also by the Terminus mercenary groups and even aliens were using the Human designed craft. However she had not had a chance to go over the crafts specifications so she was unaware what it was truly capable of. Though if she was honest she would probably get a better evaluation by asking the pilot over reviewing the specifications. With one final look out over the cargo bay she turned and made her way through one of the two doors that lead to the actual engineering section.

The first thing that Lillian noticed as she stepped through the doors, which looking at reminded her that she would need to speak to Miranda about having the Cerberus logo removed from everything, was the soft hum of the Normandy's beating heart. Her Mass Effect cores steady hum was like music to Lillian's ears, it felt as though it had been an age since she had last sat and listened to what she considered to be one of the most relaxing noises in the known galaxy. She simply stood and listened to the gentle pulsing on the core for a moment before she realized that she was being watched by two individuals who were currently occupying the deck. With a smile Lillian made her way over to the engineers, to introduce herself and learn more about this amazing drive core.


It had taken slightly longer than she had initially thought it would to get round the whole ship. Most of the time had been spent with her engineers if she was honest however. Both Kenneth Donnelly and Gabriel Daniels were ex-Alliance and seemed to hold no ill will towards any of their alien allies, in fact they were here because of her and her alone. That had been unexpected, but a theme she noticed as she went though the ship introducing herself to the crew. Not that the hero of the Citadel needed an introduction, but she liked to do it. It was only the mess sergeant who seemed to have any sort of trouble with aliens, though from what she could see it was not exactly a deep seeded hatred, more a mild dislike at best. It was not exactly what she was expecting from a famed Human centric organisation such as Cerberus.

What she was very appreciative of however was the support that she seemed to have from the crew with regards to her claims about Reapers and the dedication they were already showing in their desire to hunt down the collectors, as it seemed that quite a few of them had lost friends and families to the attacks already. To those that had she made a very clear promise, she would save them. And if she could not then she would make sure that they were avenged, it seemed to be what they needed to hear.

After a round of the ship, upon which she had ended up in the med bay and had been reunited with the old friend of Karin Chakwas, who had insisted on a quick check up. The results had been what she was expecting, she was in complete health. After a quick chat she headed up and spoke to her illustrious pilot who had more than a few things to say about EDI always watching over him. Shepard had reminded him that the AI was there to help and not take over. The conversation had then simply turned to a trip down what seemed to her a very short version of memory lane, because even though she wanted to spend more time talking to Joker, she needed to get Miranda and Jacob briefed on where they were headed.

Sitting in the briefing room, Shepard was going over the dossiers that had been forwarded to her by the Illusive man as she waited for the two Cerberus operatives on-board to arrive. As if on cue Jacob and Miranda walked through the door at the same time, Shepard wondered if she scared them. After all Jacob had been in the armoury which was right next to the briefing room, there was no reason from him to arrive at the same time as Miranda. Unless the two of them had wanted to arrive together as a show of force. However it was not as though it actually mattered. She waited before they were both seated, the two of them electing to take seats that opposed each other.

"I have now had a chance to look around the ship and there are a few things we need to discuss." Shepard started. Miranda's face seemed to be slightly in shock, an emotion that Shepard was sure that she was not used to feeling, on the other hand Jacob was as stoic as she expected him to be.

"Like what Shepard?" Due to Miranda's shock it was Jacob that ended up asking the question.

"Well for starters all of the Cerberus stuff has to go," She was beginning to enjoy the look of terror on Miranda's face that slowly seemed to be twisting into anger. "I don't care what it is on, doors, hull, uniforms, it all has to go. I am not flying around the galaxy with that crap anywhere near me."

"Commander I must protest," Miranda started. Shepard let out a silent sigh. She had known that Miranda would be the one to argue the point afterall. "This is a Cerberus vessel..."

"I don't care Operative Lawson. Cerberus are a known organisation, and labeled as a terrorist one at that." Shepard interrupted her. She didn't know if all the accusations thrown against Cerberus were true or not, but she knew that having the symbol on the ship was just asking for trouble. "True or not it doesn't matter. People will associate the emblem with terrorism. I don't want that, we need to get it scrubbed."

"Very well Commander..." Miranda answered through gritted teeth. "I will arrange it the next time we dock somewhere with the facilities to cater to that request."

"Good, I have other concerns but for the moment they can be left to rest." She lay the dossiers out in front of her.

"I take it we know where we are going then?" Jacob asked.

"Of the dossiers we have, I would suggest that we start with Mordin Solus, the Salarian." Miranda stated, trying to regain a direction with the conversation and some medium of control. "We need someone who can counter the effect of this Collector problem and he is just the man to do it."

"I agree Miranda, the good Doctor will make an excellent addition to the crew," Shepard smiled slightly at her XO, who made no attempt at returning the gesture.

"What about Archangel Shepard. From what I see he would make a great addition to our effective fighting force." Jacob added in his own opinion.

"Again a good assessment Mr Taylor." Shepard didn't really want to appear as though she was picking favourites, in a ways she wondered if this was what it was like having kids. "Either way we are heading to Omega first. So make sure our gear is good to go, I am not expecting it to be an easy ride."

"Aye aye Commander." Both the Cerberus operatives replied, leaving a slight smile on her face.