Disclaimer: I do not own Mass Effect but all original content is mine.

This is my first fanfic so please be nice, but also let me know what you think :)

Chapter 1: Plague and the Reaper

Earth Standard Date: 4th March 2059/Citadel Standard Date: 1183

Earth:

Alarm rang throughout the subterranean base as several soldiers ran down the long corridors that run right to the surface access elevator. Stopping 25 meters from the elevator doors, the soldiers set themselves up in defensive positions as they primed their assault rifles and submachine guns. 30 meters behind them a set of thick steel door closed behind them. The soldiers were all wearing power armour which was completely sealed from the outside world, mainly to prevent infection. Supplementing their rank were several mechs with assault rifles all of which were controlled by the base's AI. The Mechs were slightly smaller than the average person; they are designed to be as strong as the average human. The base itself was dimly lit, walls were nothing more the white concrete with the occasional sign painted on them, cables and pipes ran along the top of the ceiling. The air was dry and warm. The floor was a thick steel mesh over what resembled an open drainage pipe which was bone dry. Along with the alarms ringing the noise of; the air ventilation, muffled movement of equipment in the distance, the soldiers shuffling and priming their weapons could be heard. Then as the main elevator opened, the soldiers and mechs opened fire at the disease ridden people that charged out of the elevator. To call them people was now incorrect; they had been lost to the disease that was devastating the surface. The infected still resembled people, except their skin was now greyish-white and covered in large tumorous boils, which on occasion leaked black liquid. Their eyes were completely black and they released horrifying shrieks. Bullets streamed across the hallway into the crowd of infected and about a minute later the last infected died. The Soldiers and Mechs remained on alert as three Mechs with flamethrower began to cleanse the hallway in front of the main group with fire. The infected bodies crackled under the white hot flames. If it weren't for the Soldier's power armour then they'd cook. As the Mechs burned the area in front of them to the 5x5 meter elevator, the lead Solider walked a meter away from the fire and main group; finally coming to a stop he placed his right against the com unit inside his helmet.

"Aaron, how the hell did they manage to get down the access elevator?" He said in rather concerned and annoyed voice.

"It appears the infection is much smarter than we thought, Dave. Amanda has ordered that once you and your squad has passed through decon, you're to get to your stasis pod." The AI replied in a British accent and unconcerned tone.

"Roger that" Dave simply replied as he turned to the rest of the squad, coming to a halt in front of them, all eye were now on him. "Well since how we've had a breach, the plan has moved forward. If we get through decon with a green light then head strait to your stasis pod."

The group gave him a nod has the head back to the steel door. The steel door moved to the right into the wall and then closed behind them once the soldiers and mechs were inside.

"Decontamination in progress" Aaron announced as they were all sprayed with super anti-septic gas, and liquid. The liquid drained though the floors steel mesh into the drainage pipe that was specially designed to be not be a part of the rest of the drainage system, but rather lead the liquid straight to the incinerator. After that hot gas blew in all directions to push off any remaining liquid. Then finally white energy field descended down from the ceiling until it reached the floor and then went back up again. The whole process lasted fifteen minutes

"Okay you guys are clean" Announced Aaron rather suddenly as the opposite door leading into the base slide open.

The Control room was deeper underground and was the heart of the complex. The room itself was busy as personnel went about sorting out the final preparations for long term stasis. The room was 12x8 meter room, the walls were the same white concrete as the rest of the base, and the air was warm and energetic. Various touchscreen computer consoles lit the room up, which were supplemented with holographic displays. The whole room was lit up in a sky blue light from the computers and displays. The blue light bounced off the walls and gave the whole room an eerie yet mystical feeling. The large room had only one entrance. The consoles were positioned so user at the stations would face the entrance. At the centre of the room was the 'central station' a large computer console which could control, in theory, everything in the station. This console was semi-circle shaped and stood directed at the opposite end of the room from the entrance. A cylindrical pedestal was built in the central console, and was positioned to be closer to the entrance by half sticking out the central console. The console was about a meter high whilst the pedestal was about 10cm higher. Amanda was at the 'central station' prepping all the systems for their extended sleep in stasis.

Amanda was 5ft 10in, which was quite tall for women. Her skin was pale white due to living under ground for a year however it only highlighted her long dark orange hair which reached her shoulders, her deep green eyes the could pierce into your sole with the right look and small nose. She wore her custom power armour, excluding the helmet which was on the computer console next to her. Her armour custom painted to be white with a red stripe leading down the arms, legs, chest plate and back.

"Aaron, how long before the virus on the surface dies out?" Amanda quickly asked as she was doing system checks.

"I'd say about 850 - 900 years, but just to be safe why don't we make it a 1000 years?" Aaron replied as his avatar rippled to life on the pedestal. The hologram was about a meter high and was blue. It was almost see through, but you could clearly make out details on the hologram. If it weren't for the hologram being see through and blue then you'd clearly be able to see that Aaron's avatar is that of black British decent. The avatar had short hair and was rather thin, he mainly lean to one side with his arms crossed.

"A 1000 years! Can the pods even keep all of us alive that long?"

"It's possible, although I'll to utilise the geothermal plants in sequence to avoid them burning out, but I think I can do it"

"You think?" Amanda asked as she stopped, looked up and raised an eyebrow at the holographic avatar staring back at her with a very bad pokerface.

"98% certain… Look don't worry, I'll find a way – just don't be surprised when I've cannibalized the now critical systems" He replied with a touch of confidence.

"Well fair enough, tell everyone to get to their stasis pods."

"Already done" Aaron said as everyone in the base received the message on their com units.

It only took 15 minutes before everyone except Amanda was in their stasis pods, Amanda was doing last system checks before she took her helmet and placed it in a storage locker beside the only stasis pod in the command centre, it was direct next the 'central station'. After sealing her helmet away in the storage locker she opened the pod and placed her assault rifle in a specially designed holster before putting making sure her pistol was at her side and armed. She step inside and the door closed in front of her.

"Aaron, confirm that everyone is safely inside their pods?"

"Confirmed Commander"

"Then begin the localised neutron purge, outside the facility."

"Okay…. Done" Aaron replied smugly

"Okay, keep everything in order will I'm out"

"No promises…" Aaron replied playfully

"Son of a bitch thinks he's funny…" Amanda muttered before she put on her breathing mask and the stasis fluid filled the pod and then without warning everything froze. Amanda fell asleep just at that moment, and then time stood still inside the pod.

The base's light shut down, along with all the non-critical systems

Citadel Date: 2183

The Citadel was busy with activity as per normal, the long arms of the Wards were lit up with city lights except from the area were the local star in the nebular shown on them. The Citadel defence fleet could faintly be seen in the nebular. The only thing different about the ships around the Citadel was a few Batarian ships orbiting outside the station.

The Citadel tower was the main focus today as the Council were finally dealing with the Batarians pushing their luck. The three Councillors stood at the podiums slightly looking down at that the Batarian ambassador and his assistants.

"The Batarian government has been warned not to attack Citadel colonies ambassador." Councillor Tevos stated calmly towards the Batarian that was now giving her a dirty look.

"Councillors please, the Hegemony has nothing to do with the independent slavers" Retorted the Batarian ambassador whilst staring directly at the near 1000 year old Tevos.

"Then how come captured slaves from Citadel space end up at Hegemony slave market?" Councillor Valern asked in his rather quick tone.

"Well the Hegemony was raiding the pirate slavers and taking them into better care" coyly stated the ambassador

"Bullshit! Lie to your people if you want, but don't lie to us!" Growled Sparatus before adding "If the Hegemony continues raiding Citadel colonies then direct intervention maybe necessary"

Councillor Tevos quickly gave Sparatus scolding look before turning her attention back to the increasingly looking angry Batarians.

"What Sparatus meant is if the Hegemony does not stop raiding colonies in Citadel space then you will leave us no choice but direct intervention."

"You are denying us of our cultural heritage! This is offensive!" Barked the Batarian ambassador

"You have been warned" Tevos stated calmly before noticing her fellow councillors gave her a gesture that they were ready to wrap this meeting up, clocking on to this Tevos stated in the same calm tone "This meeting of the Council is adjourned"

The Batarians stormed out as C-sec guards escorted them back to their ships. The Council stepped inside their private chamber. Valern simply sat down at the table in the centre of the room and began checking up on events from various STG teams on his Omni-tool, whilst Sparatus grabbed a protein bar, sat down at the table un-wrapping the bar. Tevos was the last in and as soon as the doors were closed she gave Sparatus a look that if looks could kill, would have vaporised him there and then.

"Threating war with the Batarians? Do you have any idea of the political ramifications of that statement?" Tevos barked at Sparatus, who was now half way through his protein bar.

"We were all thinking the same thing. The Batarians have been pushing their luck for years now and besides it's not like we can't handle them." Sparatus indifferently replied

"Can handle Batarians yes. But not both them and Terminus Systems."

"Valern is right, a lot of Batarian operate in the Terminus Systems and I for one don't want to be dragged into a galactic war because you don't bother to check with us before making threats!" Tevos' biotics started to show as she was surrounded in field of dark energy

"Look okay, I hear what you are saying. Just set up a diplomatic meeting later on in the month with the Batarians again and try to came things down"

"Batarians pretty annoyed. Particularly with today's meeting. It'll be difficult" Valern stated interrupting the other two councillors.

"Well preventing galactic war would be prefera-" Started Tevos before she was cut off by the stations alarms.

The Citadel Mass Relay was quite for the most part, nothing had exited it since the Batarians arrived two hours ago. The Fleet was orbiting the Citadel whilst a detachment of a few frigates broke formation to escort the Batarian ships. The ships approached the Relay but before the Batarians could use it, the Relay came to life. The next moment was surreal to the Captain of the Destiny Ascension as a massive 2 kilometre long vessel exited the Relay with dozens of Geth ships. She watched as in a matter of seconds the 2 kilometre vessel ploughed right through the Batarian ships, destroying them on impact. Matriarch Lidanya could not believe her eyes as this vessel was intact. A split second latter hundreds of years of training slapped her back to reality as she start barking orders for the fleet to engage the Geth and this large vessel. She also ordered the Citadel council be evacuated and the station be sealed off.

A C-sec officer was escorting the Council down several hallways to their transport to the Ascension; the Citadel was no long safe as confirmed report of Geth on the Citadel had come over the comm.

"What exactly is going on corporal?" Sparatus asked as he briskly walked

"Geth on the stations sir. They've taken Citadel control. The station isn't closing and the Geth or advancing" replied the Asari Corporal before she stopped and offered her pistol out to the 3 councillors. Sparatus took it after a moment's hesitation.

"Geth on the station? Most concerning. How did they get aboard?" Valern asked now visibly looking worried.

"Don't know sir, first sighting was on the Presidium sir."

"Where is the rest of your unit?"

"The Geth got them Councillor Valern. I was ordered to go after council while they held the Geth back"

"How in the Goddess' name did they get there? Were they any visible signs that they cut their wa-" Tevos asked before she was interrupted by their best Spectre; Saren Arterius.

"Councillors! I'm glad you made it out alive, follow me I can get you to your transport" Saren stated in his normal sly tone

"Saren, thank the Spirits you're here, we need to get out of here" Sparatus stated as he checked the thermal clip in the pistol.

"The main route is crawling with Geth; however I've found us an alternate route. Follow me."

The group briskly walked down several hallways leading away from the main fighting. That's when they got a view of the Wards closing, which normally would be a good thing however the sight of the 2 kilometre vessel inside the arms made the situation even worse.

"By the Goddess, look at the size of that ship. It's huge" stated the Asari corporal who was in awe at the sight of it.

"Councillors and corporal wait here, I'm going to scout ahead" Saren said before turning away and jogging down the hallway and taking a corner.

"This is bad, the Citadel arms are closed, how are we going to get off the station? And way is the big vessel docking with the Citadel tower?" Sparatus growled as became noticeably nervous.

"Sirs and Ma'am, we need to remain quite otherwise the Geth will hear u-" The Corporal quietly began before her barrier and head exploded all over the 3 now shocked Councillors before collapsing to the ground revealing several Geth and Saren rushing towards them. Before Tevos and Sparatus knew to Valern was hit several time in the chest before collapsing backwards. Instinctively they both ran for some nearby cover. To call it cover was a bit too generous, it was a small steel table turned over, but they really didn't have a lot of options. Instinctively the moment they were under cover Sparatus popped out of it and began to fire at the closest Geth whilst Tevos used a biotic throw on another one. Two Geth down, only a few more and a rouge Spectre to go. Sparatus checked his thermal clip, only a total of 15 shots remained out of both the extra thermal clip and the current clip. Again popping out of cover he fired at the nearest Geth trooper, downing it quickly before Saren's assault rifle broke through his barrier and ripped right through his left shoulder, causing Sparatus to get back into cover.

"Fuck!" Sparatus shouted as he gripped his shoulder.

Tevos quickly popped out of cover and throw a Stasis at Saren whilst Sparatus fired from his right hand at the remaining Geth. Saren dived out of the way but now his little Geth squad had been dealt with. Saren quickly run to cover behind a wall.

"Why are you doing this Saren? This is treason!" Tevos shouted behind her cover as she applied Medi-gel to Sparatus' shoulder.

"Treason? I'm trying to save lives. The Reapers are too powerful to be stopped. I'm forging an alliance with them in order to save more lives than have ever existed." Saren barked with defiance as he lent out and fired a quick burst at the table and then going back into cover.

"Reapers? Saren that thing is obviously a Geth ship and how is killing everything on the Citadel, saving lives?" Tevos shouted

"Some sacrifices are necessary in order to achieve perfection!"

"As soon as he comes out of cover throw a stasis on him, I'll do the rest" Sparatus whispered before popping out of cover and aiming at Saren location. Tevos popped out and got ready to freeze the rough Spectre.

"Saren, I don't know what the Geth have done to you but we can help you!" Sparatus shouted

Saren leant out with his assault rifle primed but before Sparatus could fire of a shot he stopped. He couldn't move. Tevos felt a sharp pain in her back and blood run down her. She'd been shot but not by Saren. She turned around to see a powerful Asari, MatriarchBenezia. Tevos gave her a look of shock, anger and confusion before Benezia lifted her pistol to her head and fired. Saren jogged up to them and aim at Sparatus, who was still unable to move. The moment the Stasis stopped Saren unloaded half a thermal clip into Sparatus before heading to the Citadel tower with Benezia.