Chapter 1 A Choice

The space around Earth was filled with the remains of ships from every race in the galaxy as the finally battle between advance life of this cycle did battle with the force sent to harvest them, the reapers. These massive machines had removed all advanced life in the galaxy multiple times and now they were up against the humans, the rest of the council races and many others. Their final weapon had been deployed; the massive crucible which when combined with the massive space station called the Citadel would send a pulse of energy out that would stop the Reapers. Standing at the controls of the weapon in a position that no organic life form ever stood before was Council Specter and Commander of the Human Alliance Vessel SR2 Normandy, John Sheppard. His armor had been burned away by a head reaper Harbinger beam, likely Harbinger itself. For a moment he just looked up at the destruction around him as the holographic image of the boy he had seen killed all those weeks ago when he fled Earth to save it appeared.

"Who are you?" asked Sheppard to the boy

"I am the catalyst." answered the boy

"I thought the Citadel was the Catalyst." said Sheppard as he held his side with one arm and his gun in the other.

"No, it is just one of many vessels for me." stated Catalyst "I am the one who created and controls the Reapers."

"Then you can stop this." said Sheppard as he gripped his side in pain, his black armor stained red with his own blood.

"I can but it is yet to be seen how it will end." stated the Catalyst

"Why are you doing this?" asked Sheppard to the blue holographic manifestation of the Catalyst. "Why did you create the Reapers?"

"They are my answer to the organic problem." stated the Catalyst as an Alliance cruiser exploded nearby however the massive mass effect field of the Citadel protected them from the exploded.

"The organic problem?" asked Sheppard

"Without the Reapers to harvest them, advance organic life will make synthetic life and they will destroy each other." stated the Catalyst "The Reapers remove both advanced organic and synthetic life and clearing the way for the next generation of races."

"I have to admit Commander Sheppard you are the most interesting organic I have ever come about." explained the Catalyst "I have seen many cycles of life but never has an organic been able to unite both organic and synthetic life without enslavement."

"Why is that interesting?" asked Sheppard

"It is something I believed to be impossible it must be studied to see if there is new answers to the organic question." stated Catalyst

"I am not sure I totally understand." said Sheppard as he looked around for some controls to activate the crucible.

"You are looking for a way to destroy or control the reapers." stated the Catalyst as suddenly a holographic computer screen appeared in front of Sheppard "This control panel will allow you make the choice however you need to understand the truth before you make your choice."

"What truth?" asked Sheppard as a holographic map of the Milky Way galaxy appeared, all over the galaxy was thousands of red dots. He didn't need to be told that those dots were marking the location of Reaper capital ships.

"This map shows the Reaper forces in this galaxy alone." stated the Catalyst

"Wait this galaxy? You're in other galaxies?" asked Sheppard as the image zoomed out as more galaxies came into view each with red dots in view. Sheppard's eyes widened at the scale of the reapers force, the milky way galaxy had become nothing more than a dot on the map of thousands if not a hundreds of thousands of galaxies appeared before him each with red dots in it our waiting just outside. It was like a giant web of red dots each representing a Reaper fleet. Finally it stopped moving out as Sheppard got a sense of the scale of the Reaper force; they had only been fighting the tip of the iceberg.

"Yes, did you really think this galaxy was the only one I was in." explained the Catalyst "Each galaxy I control have its only Mass Relay network and a Citadel just like this one. I control it all from my own station in Dark Space."

"My God." stated Sheppard as he tried to image how many reapers were really out there.

"Your idea of God isn't important only thing that matters is the answer to the question may have a new answer." stated the Catalyst

"What Question?" asked Sheppard

"Can organics and Synthetic life live together." stated the Catalyst "The old answer was to make sure life carry ones every once in a while the Reapers must come and clear the way for new life to rise. We have done this over millions of years but not anymore."

"What has changed?" asked Sheppard

"You are here." stated the Catalyst "Never before has an organic reached this place and never before has the galaxy including organics and synthetics come together. In every cycle before organics refused to unite with synthetics and spent the time fighting each other as my forces moved in. An entire galaxy coming together as equals both organics and synthetics has never happened in any of the galaxies this means I must reevaluate my base assumptions just like you must reevaluate yours."

"What does that mean?" asked Sheppard

"You believe from this station you can destroy or control the Reapers and you are correct." stated the Catalyst "However it you will only control or destroy the forces in this galaxy and I will send reinforcements to finish the harvesting, the nearest reserve fleet is only three earth years away and others will be behind them. This station will not be able to stop them."

"So it doesn't matter does it?" asked Sheppard "If I destroy the Reapers more will show up and if I control them you will just overwhelm them."

"No, your choice matters because there is a third option." stated the Catalyst "One that may allow your races to move on and allows me to see if there is a peaceful answer for the organic and synthetic question."

"What is that?" asked Sheppard

"You must decide what to do. You know two of the three choice the final choice will be the hardest to deal with." stated the Catalyst "Let the Reapers go."

"What?" asked Sheppard

"If you let the Reapers go we will stop the Harvesting and maybe a New Balance will be created." stated the Catalyst

"A new Balance?" asked Sheppard

"Yes, I will monitor you and if you prove the inability to have organics and nonorganic live side by side then I will send the Reapers back in." stated the Catalyst

"If we live in peace then you will not return?" asked Sheppard

"Correct." said the catalyst

"So one war between organics and synthetics could doom us all?" asked Sheppard

"No, I look at trends, outliers are always present. In other cycles and in other galaxies there has been wars even between two synthetics races or mercenarily groups made out of organics and synthetics. The question is if you are able to live in peace together more often than war." explained the Catalyst

"So my choices are either destroy or control the Reapers in this galaxy but others will come as soon as they can or let the Reapers go and as long as we stay at peace you will never return?" asked Sheppard

"Those are your options." stated the Catalyst. "Now what do you choice? Place your hand on the control and speak it out load and I will broadcast your order though out the galaxy."

Sheppard lowered his head as he thought for a moment as another Reaper exploded followed by an Asari dreadnought before placing his hand on the holographic computer.

"Send the Reapers back into dark space and give peace a chance." ordered Sheppard

"Very well." stated the Catalyst as massive amount of blue energy began to gather near the center citadel at the crucible "All Reapers that can move will return to dark space all ground soldiers and downed ships will be self destruct the moment they get the transmission."

The energy shot off covering the entire sole system before entering the massive structure at the edge of the solar system known as the massive mass relay which contented Earth to the rest of the galaxy when the energy hit the relay the system built up power before shooting the energy out thought out the relay system spreading the retreat order to all Reapers in the Galaxy. Around Earth the Reapers who had at one time been killing and harvesting every living thing on the planet took off heading into space faster than ship in sword fleet could move.

"Admiral Hackett this is Sheppard do not fire, the Reapers are retreating out of the Galaxy." stated Sheppard over the communication link "I say again do not fire. The Reapers are leaving we have a peace treaty."

"This is Hackett stand down." stated the admiral's voice

"Thank you." said Sheppard as he looked at the holographic boy as the energy died down as the citadel began to return to its normal position

"The choice of whether or not we return is now up to your people." stated the Catalyst "Will you live in peace or will the harvest have to start a new. The choice is yours and your children's now."

Commander John Sheppard opened his eyes to see the streaks of blue light through the skylight that showed that his ship was moving faster than light. His breathing was heavy as he remembered the events of almost two years ago and the battle for Earth and the Galaxy. The memories from the battle and his choice still haunted his dreams and they would probably be there for the rest of his life along with the dreams of his lost friends, his squad mates and seeing whole worlds burn. He wondered if made the right call, if he should have destroyed the Reapers instead of letting them go. They were almost five years out from the battle but Earth like Palaven, Thessia and almost every other populated planet in the galaxy lied in rubbles; it would take decades if not centenaries to rebuild what had been lost.

Slowly John Sheppard got out of bed putting on black boxers which had found a place on the floor next to black lacy bra. He turned his head to see the sleeping face of his squad mate and lover Ashley Williams sleeping in the bed with a smile on her face. Slowly he moved up to the office area of the captain's cabin. He turned on the holographic computer as he looked at the time; they still had a couple of hours until they made it to their arrival at the Citadel. It was their first stop on a victory tour that would take them all over the galaxy finally ending at Earth on the anniversary of the battle for Earth and the end of the war.

"Is something wrong Skipper?" asked Ash as she sat up in bed.

"The speech." answered John as he looked at the prepared marks that some alliance speech writer had wrote for him "I am a soldier Ash not a speaker."

"Really because I remember you giving on hell of a speech on Earth before we charged into battle." laughed Ashley "Mr. our bond is stronger than any weapon or any ship."

"That is different." answered Sheppard "Here everything I say has political ramification."

"John, you united the Galaxy, brought Turians, Krogans and Salarians together in an alliance not to mention making peace between the Geth and Quarians." explained Ash "You can handle a room full of politicians."

"I guess." said John

"Now turn that computer off and come back to bed." ordered Ashley as John turned the computer off and headed back toward the bed.

Sooner than anyone wanted the Normandy exited faster than light speed a few hundred kilometers from the mass Relay at the controls of the SR2 Normandy sat Jeff Moreau nicknamed Joker.

"Once again a perfect exited from FTL." said Joker as he guided the Normandy toward the massive space station called the Citadel.

As the Normandy flew though the open arms of the Citadel toward the space port, commander Sheppard appeared behind the cockpit seat dressed in his black and blue N7 armor.

"How are things Joker?" asked Sheppard as he crossed his arms over his silver white and blue armor.

"Good, it looks like the keepers have already rebuilt everything the Reapers destroyed when they attacked." said Joker as the massive high rises of the citadel flew by "If only we had those little bug things for the rest of the galaxy."

"I would rather rebuild Earth with our own hands." stated Ashley as she walked up also in her own blue armor. "We don't know if those keepers are reporting to the Reapers or something."

"Still it would make life easier." Stated Joker as they neared the docking port, even from a distance they could see the massive amounts of people gathered to welcome the heroes of the Galaxy to the Citadel.

"I think you will need that armor just to get though that crowed." laughed Joker

"The council wants us dressed in the armor we went into battle with." explained Sheppard "Part of their grand celebration."

"I would rather be celebrating then dyeing." laughed Joker as the Normandy pulled into the docking bay, the docking arm extending.

"Well here we go." said Sheppard as he turned and headed toward the airlock.

"Sir, I am getting a message from Commander Bailey." yelled Joker before the airlock could open.

"What is it?" asked Sheppard

"He is sending cars over to take you to the council meeting room." stated Joker "They are willing to go in though the shuttle bay if you want to avoid the crowd."

"Tell Bailey I owe him one." stated Sheppard as he moved back down the long neck of the Normandy and toward the shuttle bay. "Aren't you coming Joker?"

"And miss the chance to see some of my adoring fans?" asked Joker

"Go right ahead." said Ashley

When the two of them reached the shuttle bay they found four C-Sec police cars waiting for them.

"Welcome back to the Citadel, Commander Sheppard." said Bailey as he offered his hand.

"Glade to be back, I haven't been here since they moved her out of Earth orbit." said Sheppard

"Well it's good to have you back." said Bailey

"Glade to see you made it off the station before the Reapers took it." stated Sheppard as he shook the C-Sec commander's hand.

"It wasn't pretty but we got out as many as we could." stated Bailey as the two of them got into one of the cars which took off toward the Citadel tower "They just hit us so hard."

"Well it looks like almost everything is back now." said Ash from the backseat.

"Expect the people, those can't come back." explained Sheppard

"We took 98% casualties when they attacked." explained Bailey "If I hadn't been in a meeting with the council about the state of readiness of C-Sec I would have been among the dead. Sometimes I wonder why I was spared when so many including my friends were taken."

"Honor them by rebuilding everything we lost." stated Sheppard as the Presidium came into view. The massive fountains and walkways had already been rebuilt as good as new. Already people where gathering around the base to the citadel tower where the council holds their meetings and where the first event in the victory tour would begin.

"It looks like time Square during New Years eve." stated Ash as the crowds began to grow when each shuttle arrived.

"We will be taking you in the back door." explained Bailey as the car moved to the rear loading area of the Citadel tower. The line of cars came to a stop as Sheppard stepped out of the car only to come face to face with the members of the council which ruled over most of the Milky Way galaxy.

"Council woman Tevos." said Sheppard as the offered his hand to representative of the oldest and most advanced race in the galaxy, the Asari. The mono-gender race of what appeared to be blue woman which lived for around a thousand years where one of the two founding races of the citadel council.

"Sheppard we owe you a dept that we can never repay." stated Council women Tevos

"Agreed." stated the second member of the council the female Salarian Valern who representative the second founding race of citadel council the amphibian race of the Salarians. Her deep black eyes looked at Sheppard who she had once tried to bribe to stop the genophage from being cure. Sheppard looked down the line at the faces of the new council that would hopefully keep the peace in the galaxy. The Turians councilman Sparatus had returned.

The new human councilman Dominic Osoba who he himself had brought his dead son's dog tags to him now stood as the full time representative of humanity on the council. Standing down the line was the representative of the other new races which had rose up to take either a council seat or new embassy.

The warrior Krogans who had rapidly grown after the cure of the genophage now had an embassy on the citadel and that rapid growth was major worry to some of the other races. The jellyfish like Hanar representatives not only their race but the Drell who lived mostly on the Hanar home world with a position on the council but they turned it down as they focused on rebuilding. The slow moving giant race known as the Elcor had been also been offered a council seat but they were still trying to reform their local governments so they decided to stay as an only embassy race until they could reform. He walked down the line shaking the hand or saying hello to the ambassador finally he reached the final three ambassadors.

"Admiral Shala?" asked Sheppard as he looked into the face visor of Admiral Shala'Raan a member of the Admiralty board which held the military power in the Quarian race.

"Actually it is Ambassador Shala now that I representative my people and part of Rannoch." stated Shala as Sheppard looked to her right only to see a Geth Prime standing there.

"Greetings Commander Sheppard I am Legion." stated the Prime as Sheppard raised an eyebrow

"Legion?" asked Sheppard

"Yes, that is my title." stated the Prime "In honor of the first Legion who gave his life to give us all intelligence all leaders of the Geth conscious are given the title Legion."

"I see." stated Sheppard as he looked to the last member of the council space. Standing there was a member of the insect like race of the Rachni. The Rachni while a member of the council space didn't have any members of its race on the citadel itself preferring to stay on the home world to rebuild. Only when needed did a Rachni ship carrying either the last of the original queen or one of the new queens which had been born after the war would come to give its voice to the council. The Rachni would watch the ceremony before returning back to their home world.

"Well commander are you ready to begin?" asked Council woman Tevos

"I only had a few members of my team onboard the Normandy." stated Sheppard "I would like to spend some time with them before the speeches."

"The rest are waiting for you." explained Sparatus as they stepped into the elevator before going up a few levels to reach a large waiting room. The moment the doors opened he saw that the room was filled with members of the crew dating from the first flight of the Normandy to Eden Prime to the attack on Earth. On top of that were people he had met on his travels though the galaxy. Almost instantly his squad mates from his missions to take down the collectors and taking back earth moved toward him.

"We will begin in half an hour so enjoy the time with your squad." stated the human councilmen Dominic Osoba as the council members moved off leaving Sheppard and Ashley with their teammates.

Well I hope you liked the new ending I created for Mass Effect 3, I would hope that you keep on reading. Thanks Wilkins75