A/N: So here it is. The rewrite of Nano Effect. I hope that you will find it better than my last version. As always thanks to DN7 who is constantly there to make sure my stuff makes sense and that I don't cause NE to crash and burn.

Disclaimer: Last time I checked I don't own Mass Effect or Crysis. If I did then I would make a Mass Effect/Crysis game. But I don't. Bioware, Crytek and EA do.

The Beginning

A masterpiece. That's what the Normandy is. A masterpiece of both turian and human engineering. I thought to myself, listening to the soft hum of the drive core as I walked towards the cockpit. The noise was so quiet that I could only hear it due to the sound enhancements of my Nanosuit. Which is another example of an engineering masterpiece, albeit on a completely different level.

My name is Martin Duncan, Director of CryNet Systems and it's subdivision CryOps, as well as the CryNet Phantom codenamed 'Wraith'. I can count on one hand the number of people who know of this dual identity, most of whom are a part of CryNet. CryNet is a subsidiary of the Alpha Tech and Sciences Corporation which was founded shortly after the discovery of the Prothean ruins on Mars in 2148. CryNet itself was founded in 2162 after ruins of a civilization far older than the Protheans were discovered, and as such was devoted to the study and understanding of the civilization we have come to call the Ceph. Once we had an operational understanding of their advanced nanotechnology, CryNet was able to quickly climb the galactic corporate ladder and claim a spot amongst the most elite weapons and technology development firms. This was primarily due to the development and deployment of the most high tech battle armor ever seen, the Nanosuit. With that rise in power, CryNet branched itself into three separate entities to make full use of it's new abilities.

CryOps is the most widely known section of CryNet due to their handling of the Phantom and Inquisitor operatives. The Phantom's, such as myself, are armored with the N2, given full access to the entire CTA inventory, and have such extensive training even the Salarian Special Tasks Group has some catching up to do. We operate as individual agents or as small teams usually taking down pirates, arresting criminals across the galaxy, or doing the jobs some governments are uncomfortable with. With the aid of the nanosuit, superior training and weapons, Phantom's have become nearly as feared as the Council's Special Tactics and Reconnaissance (Spectre) Agents.

The Inquisitor's are the more public face of CryOps and are more recognizable in their GHOST armor. The best analogy for the Inquisitor's are that of the old 21st century SWAT teams. Using the standard galactic ranking for armor, the GHOST armor would be considered more in line with ultra-heavy armor or even powered exoskeleton, and as such allows the Inquisitors to withstand withering fire fights that most police forces wouldn't have a chance against. This has made the Inquisitor's the go to force when facing gang wars, paramilitary forces such as the Eclipse, Blue Suns or the Blood Pack, or for anti-terrorism.

Of course, CryOps does have operating protocols meaning neither the company as a whole or our individual agents can do as they wish. When we first debuted our Phantom and Inquisitor programs, the Citadel Councilors saw both an opportunity and a disaster waiting to happen. As such, the Councilors and the Directors of Alpha Tech & Sciences and CryNet both created the Citadel-CryNet Accords.

In short, it outlined the Phantom's and Inquisitor's abilities and rights for taking down criminal's or executing any paramilitary mission. We can't act against a recognized government or official with out majority authorization from the Council, or if needed have evidence to prove beyond a doubt that we were in the right. Unlike the Spectre's, we are bound by the same law we are sworn to uphold.

While we are limited in some areas, the Accords also gave us unfettered access to any Ceph ruins and the ability to research Artificial Intelligence technology which has proven vital in the field.

The other two branches of CryNet are CryNet Technologies (CryTech) and CryNet Intelligence (CryTell). CryTech, is the technology development, testing, and manufacturing arm of CryNet. The brilliant men and women here are the ones who have developed not only the Nanosuit (both the original and the newer Nanosuit 2, aka 'N2'), but the Guardian Heavy Offensive Strategic Trooper (GHOST) Armor and the entire CryTech Armories (CTA) weapon and vehicle inventory as well.

CryTell is quite simply, the only other intelligence agency that comes close to the Shadow Broker. Unlike the Broker, we forward any relevant and pertinent information to the government's who need it. Since it's impossible to simply give that kind of information out for free, we have agreements in place with various government's for payment for said information.

These three branches of CryNet are each headed by a single Director, who together with the Director of the Alpha Tech and Sciences Corporation, form the CryNet board, with the CryOps Director being the spokesperson of CryNet, so that would be me.

Getting back to the present, I was called aboard the Normandy to fulfill the position of CryNet's representative for the final stage of the ship's construction as the Phantom Wraith. As I said earlier, very few people know that Director Duncan and Wraith are one in the same, so to preserve the character of corporate official, Wraith was the one 'assigned' in the Director's stead due to a scheduling conflict. When work had begun on the Normandy project, the Alliance and Turian Hierarchy were trying to develop their own stealth ship without much success. CryNet was then contracted to help with the stealth systems, since we already had quite a bit of experience with stealth tech.

We had already completed ships with integrated stealth technology, much of which came from our study of Ceph technology. One technique we perfected was the ability to draw heat generated from ships into heat sinks, allowing these ships to be invisible to modern scanners which looked for high heat output against the cold of space.

As it were, I wasn't the only non-Alliance representative on the Normandy, a Turian Spectre named Nihlus was on board as well. A Spectre overseeing a simple shakedown run? Captain Anderson as the CO with Commander Shepard as his XO? The crew has got to be suspicious. Their suspicion would be warranted as this entire "shakedown run" was just a ruse. We were going to pick up a Prothean beacon on Eden Prime and take it to the Citadel for study. Sending Shepard might also strike others as odd for sending on a shakedown run even if they knew about the beacon in the first place, which was unlikely. The Council and the Alliance were keeping that information close to their chests, trying to keep others from getting their hands on it. The only reason CryNet knows about it is because the Council thought they might need CryNet's help with it and because we would figure it out sooner or later.

Commander Vanyali Shepard wasn't your regular XO for this kind of thing. Just about everyone in the Alliance knew her. The Hero of Elysium. The Survivor of Akuze. The Conqueror of Torfan. She held off Batarian slavers during the Skyllian Blitz on Elysium, survived her entire unit being wiped out by Thresher Maw's on Akuze, and captured Torfan despite heavy losses. She was the role model of the Alliance and the hero every soldier aspired to be. Able to survive the impossible and achieve victory in the face of defeat. Of course there were some rumors that she was assisted on Elysium by an elite covert ops specialist, rescued on Akuze by that same specialist, who then later aided her on Torfan. Rumors usually have a speck of truth in them though.

While Shepard had her adventures, I was training and doing various operations around the galaxy as the first CryNet Phantom. During a couple of these operations I worked with Shepard herself. I first met Shepard on Mindoir shortly after I had just seen my fiance, Lynna, die in my arms due to Batarian slavers. I was pretty messed up emotionally then when I saw her. Shepard was kneeling in front of the bodies of her parents and younger brother with her sister. Seeing them hardened me and I resolved that no one should have to feel the pain that Shepard, her sister, and I did that day. I brought the Shepard's to an Alliance patrol at their wish, and returned to the CryNet lab there to start my own journey.

I came across Shepard once again out of sheer coincidence on Elysium. Shepard was there on leave, as I later learned, while I was there as CryNet had received some questionable intel, but I had a hunch that there was something big going to go down on Elysium. That hunch was proven in a way even I didn't imagine. Perhaps the biggest Batarian pirate fleet ever assembled attacked one of the most prosperous Alliance colonies in the Traverse. Naturally things were crazy in the first hour of battle as the local Alliance garrison mustered what defenses they could. During the battle I heard of a lone Alliance soldier holding off the Batarians by herself. Deciding that I could best defend the colony by helping the soldier I rushed over to where she was hunkered up and was rather surprised to see that the lone soldier was actually Shepard. We quickly got a plan into action. While Shepard would be holding the choke point and drawing the Batarians attention onto herself, I would be behind Batarian lines, sabotaging what I could. When the Alliance finally arrived I disappeared, leaving no evidence of my involvement, except for Shepard herself.

A year later, Shepard's CO contacted CryNet asking us to send someone to investigate Akuze. Shepard's squad had gone dark, the Alliance didn't have anything fast enough in the region, and some bureaucrat even stopped him from sending someone himself. So, he contacted CryNet off the record and I was only to happy to oblige him. Arriving on Akuze, I found her running from Thresher Maw's. Luckily I was able to extract her before she was badly injured. I then learned what happened to her down there. Apparently there was a distress beacon that Shepard was sent to investigate. Shortly after her unit landed they were attacked by Thresher Maws. It seemed that the ones who set the beacon were also killed.I could tell that Shepard was having a hard time dealing with her losses in the shuttle ride back to the Alliance. However I couldn't do much, other than say that it wasn't her fault. I didn't know her enough. I had to leave that to the Alliance.

Then came Torfan. I was surprised to see her there after Akuze. After telling me that she been declared fit for duty, and that Torfan would be her first operation after returning to active duty. As it was, Torfan was my first "official" op with Shepard. The Alliance had contacted CryNet for a Phantom to help them take out the pirate base stationed there. It had been determined that the moon Torfan was the staging ground used for the attack on Elysium, and as such was expected to be heavily defended. Fate it seems wasn't with out a sense of irony that day. The attack was similar to Elysium, only we were the ones attacking. I infiltrated the base to provide advanced recon and sabotaged enough the enemy systems to allow Shepard to lead her unit through the base. After some very bloody fighting we took the base with no Batarian survivors, but Shepard again lost nearly her entire unit.It was there that I noticed a definite change in her personality. While on Elysium she held of Batarian forces alone, keeping them from killing Alliance soldiers. On Torfan she ordered soldiers under her command into suicidal odds without hesitation. I questioned her about her behavior, and she merely said that they were casualties of war. Akuze had made her colder, ruthless, yet having spent quite some time wearing a mask myself, I could see through hers, to see that she deeply regretted their deaths.

It was these three events, Elysium, Akuze and Torfan, that led to Shepard being on the Normandy. I figured that Shepard had to be a Spectre candidate. It was the only real plausible option. She wasn't the first Human Spectre candidate, Anderson was but he had the bad luck of having Saren Arterius oversee his candidacy. Saren was, and still is, known for being racist towards humanity and had likely set Anderson up for failure. I had high hopes for Shepard, however, knowing that not only was she the best the Alliance had to offer, but Nihlus overseeing her candidacy is also good. Nihlus does not share his fellow Spectre's hatred of humanity, instead choosing to see our potential.

That will definitely help Shepard with her Spectre status. I mused arriving at the cockpit. Nihlus was standing right behind the pilots chair in which sat the best pilot in the Alliance, Flight Lieutenant Jeff "Joker" Moreau. Staff Commander Kaidan Alenko was sitting beside him in the co-pilot's seat.

"Phantom." Nihlus greeted me.

"Spectre, Alenko, Joker. What's the Normandy's status?"

"10 minutes out from the Arcturus Prime relay." Joker responded.

I nodded once, staying silent for a few minutes. As Joker started the approach to the relay I heard footsteps come up from behind me. Turning slightly I saw Shepard approaching, suited up in standard N7 armor. Acknowledging her with a nod, we were silent as the Normandy hit the relay propelling us onward. I crossed my arms as Joker started checking off the Normandy's systems.

"Thrusters, Check. Navigation, Check. Internal emissions sink engaged. All systems online. Drift, just under fifteen hundred K. CryNet scanning vessel reports no external emissions."

"Fifteen hundred is good. Your captain will be pleased." Nihlus said turning giving me and Shepard a sideways glance before walking away.

When he figured that Nihlus had left earshot range Joker gave his opinion of the Spectre. "I hate that guy."

"You hate Nihlus, because he gave you a complement?" Kaidan asked incredulously.

"Yeah, well you remember to zip up your jumpsuit leaving the bathroom? That's good. I just jumped us halfway across the galaxy and hit a target the size of a pinhead. So that's incredible! Besides, Spectres are trouble. Call me paranoid but I don't like having him on board."

"You're paranoid." Kaidan stated seriously. "The Council helped fund this project, they have the right to send someone to keep an eye on their investment."

"Sure." Joker rolled his eyes sarcastically "But that is the official story. Of course-"

"-Only an idiot believes the official story." I cut in, finishing his sentence with my smirk concealed by the nanosuits faceplate.

"Sending a Spectre on a shakedown run is extreme. There are many other Council agents that they could send on a simple shakedown run." Shepard added, nodding in agreement.

"So there is more going on here than the Captain's letting on." Joker concluded.

Of that you can be sure Joker, I thought as the Captain's voice came over the intercom demanding a status report and ordering Shepard to the comm room. I joined Shepard as she left the bridge. With the enhanced hearing of the nanosuit I was able to hear Joker saying "Alright, Spectre or not, that Phantom is probably worse. With that suit and all." I chuckled slightly shaking my head causing Shepard to glance at me.

"What's so funny Wraith?"

"Joker thinks I'm worse than Nihlus." I stated causing her to chuckle slightly as well. "Anyway Shep, if I'm right, and I have no reason to doubt myself, you will be receiving some very interesting information in that conversation coming up. Do tell me if I'm right, 'eh?" I asked, smirking behind my mask.

"You know what this is about?" Shepard inquired glancing at me in surprise.

"I have suspicions. And my suspicions are usually correct. Well hurry up. You don't want to keep the Captain waiting do you?" I asked nodding towards the comm room.

"Fine. But you and me are going to have a talk about this." She warned, pointing at me before turning to a marine named Jenkins and the ship's doctor Chakwas.

Chuckling, I shook my head and leaned against a nearby wall. Ignoring the conversation between the three of them I opened a communication channel to Niel Teems, founder of Alpha Tech and Sciences, the parent company to CryNet and one of the other directors on the board of which I was another.

"Connection Established. External Speakers, disabled." SECOND, the Nanosuit's on board non-sentient AI told me.

"Hey Niel. It's Wraith." I said using my codename

"Wraith. The Normandy's stealth systems look solid." Niel told me.

"Yeah, but that's not what I'm calling about. Well it kind of is. But more importantly I wanted to talk about Shepard as the new Spectre candidate."

That caused Niel to pause. "What, how do you know? A human Spectre candidate? They give up on CryNet?" He asked me.

"I figured it out the moment I saw the crew roster. We knew that Nihlus was the one in charge of evaluating the new Spectre candidate so seeing him and Shepard on the roster, well, you know. As for them giving up on CryNet they must have. After realizing that they were not going to get a Phantom as a Spectre anytime soon they must have decided to try the Alliance." I told him.

"I'm still surprised that you didn't accept the offer when they first asked." Niel said.

"It wasn't right. Humanity's first Spectre can't be someone behind a mask. Besides if the first Spectre were a Phantom, CryNet would draw a lot more attention than we need and already have." I told him glancing to the side as I saw Shepard enter the Communication room.

"And we both know that the Council only wants a Phantom as a Spectre to get some more power and control over CryNet." Niel stated.

"Ain't that the truth." I muttered. "That's another reason why I didn't accept their invitation. If the Council got even more power over CryNet we could have some definite problems. The Accords were bad enough."

"True. But they did give us more official power. It might have been worth it, if we got more power ourselves." Niel told me.

"I won't argue with that, but I highly doubt that the Council would give us that kind of power. We are a big enough wrinkle in their attempts to maintain the status quo as is." I mused as Anderson walked by, giving me a nod which I returned.

"Perhaps, but they might if we could play it correctly."

"Why are you talking as if they asked us already?" I asked my slight amusement coloring my voice "We are no where near that stage yet. At the moment we cannot be mired down in galactic politics. We have enough problems keeping our tech away from rival firms."

"That's true. Anyway, Derek told me that he decided on a name for that Gauss rifle he was developing." Niel informed me, Derek being the Head of CryTech.

"Oh god. Please tell me it's a decent one this time?" I pleaded knowing Derek's past names.

"Heh, he wants to call it the CTA-2153 Gauss." Niel said chuckling.

"Ugh. That's just as bad as the other weapons he named. Seriously, who calls a new frag grenade the CTA. 30 Frag Grenade?" I complained.

"Derek does. That's who."

"Ugh. I-" I broke off as a message marked urgent popped up on the side of my HUD "Wait. I'm getting a distress call from Eden Prime! I have to see the Captain and Nihlus about that, hold on." I said turning and walking briskly towards the comm room door.

I opened the door just in time to hear Joker over the intercom saying "Transmission from Eden Prime sir. You need to see this."

When Anderson, Shepard and Nihlus glanced over at me "I just heard about that distress call as well." I stated simply.

Anderson nodded in acknowledgment before responding to Joker, "Put it up on screen."

The transmission popped up on the main screen. The sound of gunfire immediately filled the room as the video showed a smoke-filled blood-red sky. A woman in Phoenix class armor was firing at an unknown enemy. Glancing over at the camera she pushed the cameraman out of the line of fire. After another explosion the camera turned to another marine who yelled, "We are under attack! Taking heavy casualties I repeat: Heavy casualties! We can't...argh!..-eed evac! They came out of nowhere. We need-" A loud groaning sound cut in and the camera turned to look at a dreadnought of incredible size coming down to land, red lightning flashing around it.

"Everything just cuts out after that. It just goes dead." Joker said seriously.

"Reverse and hold at that ship." Anderson ordered and the video flashed back to display the oddly shaped ship.

"Do we have that profile on record?" I asked.

"Searching. . . No match found." SECOND informed us. Anderson and Shepard tensed slightly at its voice before relaxing. Nihlus howvere seemed unfazed.

"Take us in Joker. Fast and quiet. This mission just got a lot more complicated." Anderson ordered.

"A small strike team can secure the beacon quickly and without attracting attention." Nihlus said bringing up a map on his omni-tool. "I should drop first here. I move faster alone and should be able to provide reconnaissance."

"That's true. Shepard could drop here with a team." I said bringing up my own map on my visor and sending the information on to the rest. "I could drop up here on this ridge overlooking the dig-site. I would have a clear shot of the dig site and the surrounding area."

"Good idea. Captain?" Shepard turned to Anderson who nodded. "Grab your gear and meet us in the cargo hold!"

Since I already had all the gear I needed on me, I headed straight down to the cargo hold with Shepard who merely needed to grab her weapons. "I definitely wasn't expecting this." I muttered. "Here I was thinking this would be a nice and relaxing mission."

"You knew? You knew about the mission? About me being a Spectre candidate?" Shepard asked me as the elevator doors closed and the elevator began its slow journey down to to cargo bay.

"Well I knew about the mission. You being a Spectre candidate however? No, I just suspected, and you just confirmed my suspicions." I smirked at her as she narrowed her eyes. "Anyway Shep. Please don't keep me waiting at the dig site. I get bored pretty quickly."

"Hah! Just you wait and see. I'll be the one waiting!" She told me as the elevator doors opened.

"Oh really? Then last one there buys drinks!" I challenged.

"Deal. And just so you know, I want quality drinks. None of that cheap shit." Shepard said.

"If you want to pick your drink, you're going to have to get there first Shep." I told her as Anderson and Nihlus joined us. After finalizing our preparations, Joker flew us into position at drop-point one where Nihlus jumped down. Joker then flew us a few hundred meters farther and dropped Shepard, Alenko and Jenkins at drop-point two.

"Alright Captain. I am ready to drop. See you after the mission." I said giving Anderson a nod as we arrived at my drop-point. Turning, I leaped out of the Normandy while SECOND displayed a message on the HUD.

Objectives Updated

A/N: Chapter 2 is almost ready to be uploaded. So expect to see that soon. Chapter 3 is done but just needs to be edited. 4/5 are almost done. I hope to have updated NE:GC up to chapter 5 within a month but no promises. I'll probably put what I want for your OC inquisitor submissions up in a long A/N at the end of next chapter.

As it is please review and give me your feedback. I want to make this story the best it can be but it can only become that if you guys tell me what needs work!

~LEGION