A/N: Thanks to everyone who favorite, followed and reviewed this story so far, it's good to know that you're enjoying the story so far. I hope you enjoy chapter two :)

"No structural damage, no signs of battle, nothing." Miranda noted solemnly. They had arrived on Freedoms progress but a few moments ago, in search of clues as to who was behind the abduction of the human colonies. As Freedoms Progress was the latest one to be attacked, Shepard was sent along with Miranda and Jacob to investigate. They'd been told that previous investigations had ended up with no leads, but the Illusive man wanted Shepard to see just how bad things were and why the galaxy needed her.

She had expressed her feelings to the Illusive man, towards being brought back in the way that she had in a… less than civil manner. He was the one responsible for the Blacklight virus running through her, and just because she had accepted that she'd have to live with it, that didn't mean she was going to act warmly towards him or Cerberus in general. Despite its so-far harmless effects, it was still an abomination, something that didn't belong in this galaxy.

She had also quietly told herself that she wouldn't use her new abilities unless desperate circumstances pressed her to do so. She was still human and wanted to remain such, so she would do things the human way. It wasn't the easiest way to do things, but it made her feel more secure mentally, knowing that she didn't have to actually be what she had become. It would just require the willpower to do so.

This first mission was an excellent way to test that will.

Shepard and her squad had so far killed off a few groups of mechs, which was strange as they were programmed to protect the colony, a human colony. They should've identified them as non-hostile, which left two explanations. Either the abductors had reprogrammed them to attack anyone who came to check out the settlement, or someone had survived, and reprogrammed the mechs to attack anything on sight.

Shepard hoped it was the latter, but they had to be cautious as one would only reprogram to do so out of fear, making them unpredictable and dangerous.

The group came across a locked door, which raised Shepard's suspicions.

"Alright get ready to fight, but only if they fire first. We can't risk killing anyone who may have witnessed what happened here." She commanded.

Her companions set themselves on opposite sides of the door, while Sheppard worked on hacking it. Two years and they've already made better hacking equipment? Shepard noted as she connected the nodes. She'd hate to think on how many valuables would go missing if thieves go a hold of such equipment.

The door hissed open and Shepard immediately noticed four figures leaning against a desk, looking at a data pad. They snapped their heads around at the sound of the door opening and raised their weapons.

They were all Quarian, one male and three female. Yet one of the females looked a lot like…

"Tali?" Shepard asked incredulously.

"Shepard? You're… alive?" Tali responded sounding just as surprised.

Shepard gestured for her squad to lower their weapons before moving forward to embrace the young Quarian.

"I'm alive." She confirmed softly, grinning at the appearance of her good friend. Tali returned the gesture, shaking slightly from the shock, or was it relief, maybe both?

"I heard you went down with the Normandy!" Tali exclaimed when she withdrew. "No one could find your body. There was a funeral and everyone was mourning for weeks and… and…"

"Easy Tali, I'm here now. I'm back. Cerberus rebuilt me over the course of the past two years." Shepard explained

"Your working for Cerberus now?" Tali repeated, sounding shocked, "Isn't Cerberus a terrorist group?"

"Our means might sometimes be harsh but we've always had humanities best interest at heart." Miranda interjected.

"By pulling the other species down." Tali snapped. "You don't care about the other inhabitance of this galaxy, about what you're doing to them to further your own ends. All that matters to you is your goals, and you don't care how many lives you ruin to achieve them."

Miranda was about to respond went Shepard shot her a look that said not one more word, before restoring her attention to Tali.

"Tali I'm not working for Cerberus, I'm working with them, to achieve the same goal; to put a stop to the abductions of human colonies. But I promise you I'm using my own methods to achieve them. I won't be putting any innocent lives at risk if I can help it."

Tali seemed to relax a little at her words. "I know Shepard; I know you wouldn't use such harsh methods. It's just a lot to process; you working for… with Cerberus. I'm glad you're still the one calling the shots."

"I wouldn't have agreed to this plan if I wasn't" Shepard smirked for a moment before going back to being serious. "We still have a mission to do. We're trying to find any clues that could tell use who's behind the attacks."

"We were sent here to find one of our own who was on a Pilgrimage on this colony. His name was Veetor. We found out that he's holed up in a Warehouse on the far side of the settlement. We suspect he reprogrammed the mechs to attack anything that moved."

"If he was here when the settlement was attacked, he might know something that could help us find out who it was." Jacob remarked.

"We should work together to get to him, split up into two teams to separate the enemy forces." Shepard declared.

"Agreed, we'll meet you at the warehouse." Tali motioned for the other Quarians to follow, heading through the nearest door, while Shepard along with her squad took the opposing exit.

Shepard was pleased to discover that she was still able to perform at her optimal level in combat, moving fluidly from cover to cover, taking out mechs and security drones with her pistol as she went. Her aim was as precise as ever, and her reflexes greatly improved by her new DNA.

Everything seemed to move slower around her, making it easy to determine where and when an enemy would be and when they would attack. She also noticed that her hearing eyesight had greatly improved, allowing her to hear and see any hostiles and take action before they were engaged.

With these new attributes, Shepard found fighting her way to the warehouse a walk in the park. Even the heavy mech didn't pose much of a challenge.

With the last enemy destroyed, Shepard hacked the door to the warehouse, just as Tali and her squad appeared round the corner. The door slid open to reveal a room full of crates and supply lockers, with a lone Quarian at the far end, looking upon a wall of monitors, and muttering to himself.

"Veetor?" Tali asked cautiously.

"No Veetor, not here, have to hide, swarms coming…" the Quarian replied.

"Hey, no ones going to hurt you. You're safe now." Shepard explained calmingly.

No response. Shepard opened her Omni tool, and deactivated the monitors, snapping Veetor out of his apparent state of shock. He stood and faced them.

"Your human?" he exclaimed, seemingly shocked by their presence. "How did they not find you? The monsters, the swarms, they took everyone!"

"Veetor you have to calm down." Tali said firmly though not unkindly.

"You weren't here, you didn't see what happened. But I saw." He raised his Omni tool and reactivated the screens.

They now showed what appeared to be a security recording. Large bug-like humanoids walked about the settlement, carrying unconscious humans towards medium sized carrier shuttles.

"My god, those… those are collectors?" Miranda exclaimed. At Shepards confused glance she continued, "They're an alien species that resides beyond the Omega 4 relay. Few people have ever seen one in person. They work like slavers or hired mercenaries. If they're working with the reapers it could explain what happed to the colonies."

The screen panned across, bring more collectors into sight. One, Sheppard noticed, seemed to be covered in glowing embers, emitting a slight orange glow. It seemed then, to turn at look directly at the camera, at her. A sharp pain flashed through Shepards head as she locked eyes with it, and she was certain she heard a faint hissing growl. She winced as her head seared with pain, before disappearing almost as soon as it came.

"Commander, are you okay?" Jacob asked, as he had obviously noticed her discomfort.

"I'm fine. Can you tell us anything about the collectors?" she asked, addressing Veetor.

"The seeker swarms, they find you, and then they sting you, freeze you. Then the monsters take you." Veetor added. "I studied them. I recorded them with my Omni tool; Electromagnetic and dark energy readings."

"We should take Veetor and take him back with us, find out what he knows."

Tali stepped forward. "Veetor is injured! You can't interrogate him! Shepard, please, takes the data from his Omni tool but let him come with me."

"Don't worry Tali; I didn't plan on taking an injured civilian with us. We'll copy the data he's collected and let him go with you."

"Thank you Shepard. You may've been rebuilt by Cerberus, but your still you." Tali said softly. Shepard smiled at her words.

"I could use you on the team again Tali. You're welcome to come with us if you want." Shepard offered.

"I'm sorry Shepard but I can't. I have an important mission I need to complete and it can't wait. But I promise as soon as it's done I'll join you, if you'll have me."

"You'll always be welcome." Shepard smiled sadly, before embracing the Quarian.

"If I find anything that may help, I'll let you know." Tali said, before departing with her squad in tow.

Shepard took one more glance at the collectors on the screens before heading back to the shuttle.

Billions of miles away, beyond the galactic rim, in the space between galaxies, a vast intelligence stirred. Hundreds upon thousands of separate minds awoke, for the first time in 50,000 years. Coming together, they formed a single personality, one incomprehensible to any one being.

"We are Harbinger." It declared to itself. Thoughts from a thousand different minds raced before its sight, as it reached its mental influence towards the galaxy it had conquered infinite times before. "You will obey us. Assuming Direct Control!" and suddenly, it had eyes, ears, and a body. Harbinger looked upon the organic colony, as its servants hauled away those who would be the first of something greater.

"The organics think our existence is but a myth." Harbinger conveyed its message to its servants. "It is though their ignorance that they shall fall. And when they do, they will achieve salvation through evolution. They will become that which is infinitely their greater."

A wordless acknowledgement came from the minds of the servants. They understood their objective. They would bring all organic life to the pinnacle of evolution, as they were many, and the organics were underdeveloped. It mattered not how many servants fell to achieve universal order. It would be done, as it always had.

Harbinger withdrew its conscience from the galaxy before it, and finally, awoke its vessel; an enormous construct, forged from the energies of dark matter and with the soul purpose of destroying all that would oppose their genetic destiny.

The Reaper let out a low, mechanical roar, not through space, but through the slumbering consciences surrounding it. Millions, hundreds of millions of Reapers awoke, taking full command of their own vessels. They were nothing but tools however, in comparison to their leader. They were aware, independent, free of any mental weaknesses, but nothing in the eyes of Harbinger. It was the apex of its kind, ancient in thought, and form. Only the vessel known as Sovereign had advanced enough to fully understand exactly what Harbinger was.

Yet there was one greater even than Sovereign, greater, yet organic; "Shepard." The human had delayed that which should have already been. But there would be no stopping it this time. And if the human did not give in to that which it was, then she would be destroyed.

As one, the Reaper armada moved forward, through dark space, where they would finally reach their goal. And when they arrived, they would either salvage the organics, or wipe them from existence.

"We are legion. We are coming."

"I've compiled a list of soldiers, scientist and mercenaries. You'll get dossiers on the best of them." The illusive man said.

Shepard had returned to the Cerberus base immediately after their visit to freedoms progress, and informed the illusive man on what they had learned. He had then told her that they had their suspicions that the collectors were behind it all along. Shepard had grown irritated that the Illusive man had been keeping her in the dark; if he wanted her help she needed to know everything he knew regarding the mission at hand, nothing withholding.

After their brief discussion on that topic, Shepard had told him that she'd need a team to take down the collectors, as it would be a suicide mission to do so alone.

She wasn't satisfied with the results.

"I thought you'd be finding my old team, the ones who helped me stop Saren, Sovereign and the Geth. That was our agreement."

"It was your agreement with Miss Lawson, and I seem to recall her telling you that there would be 'no promises'. We did the best we could but it's been two years since Sovereign. Most of your old crew has moved on, and the others have changed their allegiances."

"Look, I don't need guarantees that they'll join me, but I still want to know where they are so I can at least ask." Shepard snapped. She was irritated because she said shed only go along with the mission on the condition that her old team would work with her. However after seeing Freedoms progress she had decided that she needed to do something, regardless on whether her demands were met or not. She felt the illusive man had planned the whole thing out. Smart son-of-a-bitch. She said, more of a curse than an admiration.

"Very well, who would you like Intel on?" he asked.

"Everyone except Tali; we already met on freedoms progress and she won't be able to join us, yet."

The Illusive man gave Sheppard what he knew about her former team. Kaiden had rejoined the alliance just as Shepard had suspected, Wrex had returned to Tuchanka in an attempt to unite the Krogan clans, Liara was allegedly working for the Shadow Broker, and Garrus… Garrus had disappeared. No one had a clue as to where he had gone; only that he had left the Citadel and hadn't been seen since.

Shepard cursed quietly to herself, and her heart sank as the Illusive man relayed the information.

"Okay fine, I'll look at your list. Is there anything else I should know?"

"Two things: Firstly, there's a Salarian scientist on Omega who may be able to find a way to protect you and your crew from the seeker swarms. Secondly, I've found you a pilot and a ship. And from what I hear, Mr. Moreau is one of the best." The connection ended.

Moreau?!

"Hey Commander, just like old times huh?" an all too familiar voice resonated from behind her.

"Holy. Fucking. Christ." Shepard grinned as she turned around, and greeted by the sight of Joker.

"That's the greeting I get after two years?" Joker smirked. "we'll at least you didn't get all sappy on me."

"How'd you end up with Cerberus?" Shepard asked as they made their way back to the main room.

"Council wanted everyone to forget everything you stirred up. The team all went their separate ways and the Alliance grounded me. two years later Cerberus offers me a job, tells me your alive and kicking and gives me a new ship. What was I gonna do? Turn it down and go back to drinking away my sorrows?"

Shepard laughed. "Did they tell you the details of my… resurrection?"

"Only a bit; I heard you've got a few upgrades, some old super chemical keeping you going."

"More of a bio weapon, they call it the Blacklight virus. They used it to knit my tissue back together properly after I woke up during surgery, then gave me more to bring me out of my coma." She explained. "It comes with a few perks, but that doesn't mean I'm comfortable with Cerberus tampering with my DNA."

"I'll keep that in mind if they ever find a cure for Vrolik Syndrome." Joker mussed.

"So you mind filling me in on the past two years?" Shepard grinned, though she was also uneasy. Tali had mentioned a funeral and she was reluctant to reopen past wounds.

Joker face immediately turned serious, even saddened. "Everything fell apart without you. When the crew learnt you were dead… I never thought I'd see a sad Krogan. Wrex was furious at first, throwing chairs around, shout into the air, hell he even threw someone across the room when they tried to calm him down. Tali and Liara were both in tears, Tali enough that I was surprised her helmet didn't fill up. Kaiden was distraught, and immediately started accusing me, and I don't blame him. If I had just left with everyone else…"

"It wasn't your fault Joker." Shepard said softly, placing a hand on his shoulder. "There was no telling whether that final beam was going to tear the ship in half or not. Blame the Collectors."

Joker nodded meekly.

"What about Garrus and the rest of the crew?" Shepard urged. Jokers suddenly flinched, which alarmed Shepard. "What happened?" She asked again.

"The rest of the crew… I didn't see them until the funeral. But Garrus was there with me and the team when they learnt what had happened. Garrus…. He just sat there. He didn't seem to react. He was just frozen. When Tali noticed and tried to snap him out of it, he just stood up and left without a word." Joker looked Shepard straight in the eye. "It was as if he had died along with you. You were like, best buddies on the Normandy."

"Surely he wasn't that upset." Shepard said uncomfortably. She couldn't imagine anyone going dead inside because of her death.

"Remember that time on the Normandy, on Galactic New Year when we all stayed up late drinking and celebrating?" Joker said suddenly. Shepard nodded.

"After everyone eventually went to bed, and it was just him and I left, he told me how much he appreciated being on the team. How much it meant to him to be actually doing something instead of sitting in front of a desk at C-Sec. He said he owed you for that. Then he went on and told me that you were the greatest friend he ever had, that you meant more to him than almost anyone else."

Shepard sat silently, not moving, not even breathing.

"Then you died, and at the funeral... everyone paid their respects, leaving gifts, praying, speaking a few words and Garrus? He left you his visor. His goddamn visor Shepard, the one that seemed to he welded to his skull, and he left it on your coffin. That's when everyone realized how broken up he really was over your death.

"A few months later he disappeared. No one knew where he went; he didn't leave a message, didn't tell anyone he was going, didn't say goodbye, nothing."

A choked sob escaped Allison Shepard then, her eyes red and watery from the tears. It wasn't just Garrus' reaction to her death that hurt, it was the probability that she'd never find him again. The galaxy was too big, what were the chances that they'd cross paths again?

Joker put a hand on Shepards shoulder. "We were all grieving when you died – hell I drunk myself to sleep every night for a week – but Garrus… he really cared about you. You were one of the few people that he cared about, and who cared about him in return." Joker said softly. "Just don't beat yourself up over this Shepard. We'll find him somehow and everything will be okay."

"Hell joker I never knew you had a sentimental side." Shepard sniffed, smiling.

"Yeah, well, someone has to keep your mental health in check. Just don't expect counseling sessions every week, I'd get a headache."

Shepard laughed at that, regaining her composure. "So anyway, you said something about a new ship?"

"Oh, yeah, you've gotta see it Shepard, its like, a hundred times better than the original Normandy!" Joker said, looking like a boy who got exactly what he wanted on a Christmas morning.

The pair made their way to an observation window as Shepard began to ask, "what do you mean Original Nor…" the words died in her mouth as she beheld the sight before her.

A ship, almost an exact replica of the SSV Normandy was docked in the hanger beyond. It was significantly bigger than its original counterpart and the design was slightly different. Another difference was the paint. Instead of white, black and red, it was now white black and orange, with the Cerberus logo painted on the wing next to 'SR2'. The name 'Normandy' was painted in large white letters along the body of the ship.

Shepard was in complete awe.

"It's good to be home huh Commander?" Joker said, smirking at Shepard's facial expression.

"They rebuilt the whole fucking ship?" Shepard croaked, barely managing to get the words out.

"The whole fucking ship." Joker confirmed, laughing. "Well with a few upgrades of course: A ship that matches its captain."

Shepard burst out laughing.

Once onboard the Normandy SR2, Miranda gave Shepard a brief tour, showing her where everything was and pointing out the upgrades. I see they decide to keep the slow-as-shit elevator. Shepard noted. The ship was much larger internally that the original, now with five floors instead of three.

After Miranda's tour, Shepard retreated to the top deck to check out her quarters. They were two or three times the size of her original cabin, with an en-suite bathroom equipped with a shower, an office area separated from the sleeping and relaxing area by some stairs and a glass shelf, and to top it off, one wall had a glowing aquarium built into it. I'll have to find some fish to put in it. Shepard thought as the tank was empty.

She went to the bed and sat down. It was comfy, a little more comfy that she was used to, as well as large. She lied down on her back and let out a yelp of panic. Where the ceiling should have been, there was a single square window looking out into the infinite expanse of space. The sight unnerved Shepard, having died after being spaced. She looked at the stars beyond the glass, remembering what it was like to be floating, to be unable to do anything, to be helpless. She closed her eyes and let out a shuddering breath.

She headed down to the CIC to more closely examine her weapons in the armory. Her set consisted of a heavy pistol, assault rifle and grenade launcher. She picked up the pistol and noted the use of thermal clips in her new weapons, as her old weapons simply overheated after a certain amount of shots. She queried Jacob on the feature.

"The old versions had an unlimited number of shots true," he explained, "but every time the weapon overheats, it can damage the internal components of the firing mechanism and burns out the energy core. So the weapons manufacturers came up with the idea for thermal clips, adding a new energy core into the gun which is a lot less expensive than replacing a standard one once it burns out, as well as the damaged firing mechanism.. As a lot of soldiers on the field usually forget to keep and eye on their overheat meter because of the distractions of combat, they're ending up with guns that don't fire right or at all."

"But wouldn't you run out of ammo and get killed anyway?" Shepard asked.

"You only need kill your enemy and take their thermal clips to maintain a steady supply." Jacob smirked. "Plus, at the time military funding was cut to repair the damage done by Sovereign and the Geth, so they needed a cheaper alternative. This was cheaper and more effective in the long run."

Shepard nodded and placed her weapon back on the table.

She went up to the cockpit and told Joker to set a course for Omega. There she intended to recruit the Salarian scientist and the vigilante Archangel.

"So how's the new setup in here?" Shepard asked, looking around.

"Shepard this ship is amazing." Joker grinned,"I've only been flying for an hour or so and this thing runs so much more smoothly than the original Normandy, and it has leather seats! So much more comfortable that the original. However there is one teensy tiny problem."

An orb of Blue light popped up beside Joker.

"Hello Shepard."

Joker groaned.

A/N: and there's Chapter two, I hope you enjoyed it. Chapter three will be more exciting and should be out within a week. I enjoyed writing the part from Harbinger's perspective, and yes there will occasionally be more of that. Please favorite, follow (or both) and leave some reviews. Thanks for reading :)