Title: Mass Effect 3: The Reaper War

Author: Tobias

Rating: M for Mature

Shepard Stats: Paragon Shepard for ME1 & ME2. Romance is Liara T'Soni in both, Wrex lives, and the council was saved in ME1. The rest you'll learn as we go alone.

Author's Note: Hello one, hello all! Thank you for stopping by to read this little story of mine! I've had this rattling in my brain since the end of Mass Effect 2. And since all of us are going to wait a year or two for ME3 I thought I might try to tide us over till then. Enjoy my friends, and I welcome any reviews.

Chapter 1

"How are we holding up Joker?" John Shepard asked, coming up behind the best pilot he'd ever known, Jeff "Joker" Moreau. Joker sighed and turned the pilot's seat around to face the Spectre. The downcast expression on his face spoke volumes to Shepard.

"We're not so good, Commander." Joker answered. "We can still fly and fight, but until we get the holes in the hull patched over, we can't use the relay to jump back. Emergency containment shields are meant for just that, emergencies."

"I was afraid you were going to say that." Shepard muttered. He sighed and ran hand threw his short brown hair in frustration. "How long until we get the holes sealed for relay jump?"

It was at this moment the hologram to Shepard's left lit up, displaying a blue sphere with a grid on the front. This was the ship's artificial intelligence, EDI (Enhanced Defense Intelligence). Full unlocked and integrated into the ship during the Collector's kidnapping of the crew, she had proven herself to be extremely loyal and helpful during the past few weeks. Shepard may have his own doubts about AI's and their motives, but he did trust EDI completely.

"Estimates from the repair crews place final repairs around 1700 hours two days from now, Commander. However, these repairs are only temporary. We will need several weeks in dry dock to bring the Normandy back to 100%." EDI said in her calm, feminine voice. Shepard swore. He knew the Normandy was in bad shape but he didn't think it was that bad.

"Not as long of a wait I thought it would be." Shepard mused. He scratched his chin for a moment, thinking. "Can we do a couple of relay jumps or do we have to dry dock at Omega? I'd like to avoid being stuck there for a few weeks."

"I think she'll hold up for a few jumps, Commander." Joker replied. "Just don't ask us to fight off the Reaper fleet."

"Our odds of surviving an assault by the Reaper fleet by ourselves are approximately three hundred billion to one with the Normandy a peak capacity." EDI chimed in.

"That's a cheery thought, EDI." Joker muttered.

"Not as cheery as thinking of you crawling threw access ducts. I did like seeing you on your knees, Jeff." EDI retorted. Both Shepard and Joker stared at the AI. "That was a joke."

"EDI," Shepard began, purposely ignoring the creepy feeling he was getting, "send a notice to everyone to gather in the mess at 1800. I want to make an announcement about what we're going to do and where we're going. Tell Sergeant Gardner to prepare for an all hands dinner then too."

"Got a plan in mind, Commander?"

"Yes and no Joker. Yes and no."

At 1800, Commander Shepard arrived at the mess to see everyone waiting for him as he expected. What he didn't expect was the loud cheer that rang out the minute he turned the corner from the elevator. He waited for the cheer to die down and couldn't help the grin that crept onto his face. He motioned everyone to sit and they all took their places, at the main tables and some extra tables and chairs pulled out for this sit down.

"We have a right to be proud of ourselves." Shepard began. "We completed our mission and saved as many lives as we could, including our own. We all made it back from the Collector's station alive, if a little beat up."

Everyone murmured their agreement and while they did so, Shepard glanced over his team. Miranda seemed to no worse for the wear, as did most of the others. Grunt and Samara were both heavily bandaged, having been with Shepard when they fought the Human Reaper.

"I've also spoken with the Illusive Man. To say he wasn't pleased we destroyed the station was an understatement, but I've done what I said I would, I've stopped the Collectors. I've paid back Cerberus for bringing me back and all they've done. As I told the Illusive Man, I'm cutting my ties with Cerberus." Shepard informed them. He held up a hand to cut off any questions. "Give me a moment to explain."

Shepard took a deep breath before continuing.

"The Normandy has been threw hell and back, as we all have. She needs a few weeks in dry dock at minimum to be back up to snuff. EDI & Joker have informed me that once the hall breeches are closed off we can do a few mass relay jumps. This is good news since we won't have to make port at Omega. I've decided our berth is going to be Illium. It's got resources we need to make repairs, it's safe enough to hire a couple of outside contractors to help speed along repairs, and we can make some coin selling some tech we've come across to fund repairs. Maybe even get even more tech upgrades to better our odds against the Reapers. But most importantly, it's got friendly faces and it's a good place for you choose what you want to do."

"What do you mean, Commander?" Miranda inquired.

"What I mean is I trust you." Shepard said firmly. "All of you."

Threw were a few sideways glances from some of the crew men towards Legion, but the Geth said nothing. It was watching Shepard intently.

"For whatever reason you joined up with me, you became my crew." Shepard said. "I trust all of you with my life and you're just as good as the crew I hand on the SR1, if not better."

Smiles were all around. That was high praise from the Commander.

"But to be honest the direction I'm going to take this crew and ship might not sit well with some of you." Shepard bluntly stated. "Breaking off from Cerberus might already be causing you to question where you fit in here. Simply put, this is my ship. When we make port, Cerberus symbols, markings, and protocols will be out the window. During dry dock I'm going to make contact with Councilor Anderson. He was going to inquire about my status with the Alliance. As you know, I have been reinstated as a Spectre. At the very least this will be a Spectre's ship, answering only to me and the Council. If I have the option and I choose to, I may be reinstated into the Alliance as well. So you may not want to stay. If you don't, I will wish you well, and we will part on the best of terms. If you stay you may have to get used to a few changes, but I want to make this very clear. If you do stay your first allegiance will be to me and our mission to stop the Reapers. So for next few days, I want you to think it over. When we dry dock, we'll be one shore leave for exactly a week before we start repairs and overhaul. I'd like an answer by the end of that week."

The mess had gone quiet by the time Shepard finished his speech. He nodded to them.

"Enjoy dinner, and sleep well tonight. We have a busy couple of days ahead of us. Good night."

Turning swiftly around, Shepard barely made it around the corner before the mess exploded in rush of voices.

Shepard cupped his hands under the faucet from his sink and splashed it on his face. He scrubbed at his face a bit and reached for a hand towel. After drying his face and tossing the towel into the laundry chute, he stared at his reflection in the mirror. His face and eyes were back to normal thanks to Dr. Chakwas and the medical bay's upgraded equipment. Even the scar from Akuze and the thresher maw attack were gone. His blue eyes were blood shot and heavy bags had appeared under them. He hadn't shaved in a few days and was well on his way to getting a beard like Joker's. Even though it was only 1900 he decided to crash for the night. A deep, long sleep sounded heavenly just about no. Leaving his bathroom, he couldn't help the jaw cracking yawn he emitted. He was just about to pull off his shirt when the door to his cabin beeped, indicating some one outside wanting entrance. Shepard groaned but turned to the door.

"Open." He commanded sourly. The door's holo-panel changed from red to green, and door shot open, allowing Legion the Geth to stride smoothly in.

"Shepard Commander, we wish to speak with you." Legion said in his robotic voice.

"Sure, Legion." Shepard said, a bit puzzled as to why the Geth was here. "Take a seat." He gestured to the couches. Legion eyes them for a moment before choosing a seat far from the Spectre. Shepard sat in his chair for the desk near his bed.

"We wish to have permission to access the FLT communications system. We would like to commune with the collective about recent events and pose an inquiry. We may also wish to converse while linked to the collective on their behalf with Shepard Commander." Legion stated. Shepard was taken back a bit at Legion's request.

"What's this about, Legion?" Shepard asked, curious.

"We wish to inform the collective about all we learned now that we have completed the mission. Then we have a request of a new mission we wish to complete with Shepard Commander's help. Communicating with the collective may take some time however and we know Shepard Commander would wish to monitor us during said time." Legion stated. Shepard frowned but nodded.

"EDI." He called to the control panel by his door. The hologram lit up in response. "Allow Legion extended access to the FTL com system while it's in my quarters."

"Acknowledged, Commander." EDI responded. There was a beep and Legion titled his head. "Legion has accessed the com system."

"Thank you EDI." Shepard said. He picked up the data pad on the Reaper data EDI had salvaged. He shot one last curious glance at Legion before studying the data again. For the next hour he would glance at Legion, who sat perfectly still on his couch. The Geth's plate on his head would occasionally move but other than a soft hum, Legion did not move or make a sound. Around 2030, Legion's head moved back to its normal position and EDI spoke again.

"Legion is still connected to the FLT communication system." EDI called from her terminal.

"Shepard Commander." Legion stated. "We have finished our exchange with the collective. Consensus has been reached on numerous concerns and we wish to speak on behalf of the collective."

"I'm honored to speak with you and them." Shepard said, setting the pad on the table. He figured being diplomatic wouldn't hurt. As far as he knew this was the only time some one had spoken with the collective since the civil war between them and the Quarians. "I hope you don't mind that my ship's AI is recording this conversation.

"We are honored as well, Shepard Commander. We have no objections to the EDI program monitoring our discussion." Legion responded, his voice taking on an echoing quality to it. "We wish to speak with you about the war against old machines and the creators. The mobile platform programs you call Legion have informed us of the events that have taken place shortly before and after its integration into your collective. Your events on the Collector's station are most impressive."

"Thank you." Shepard said humbly. "Legion was an enormous help to the mission. I hope you will allow it to continue to assist me."

"The trust you allow the platform designated Legion are impressive to us, Commander." The Collective said threw Legion. "We even understand restrictions you place upon it given your history with the heretics. However we wish to speak about them and the old machines. We have processes the information on the old machines and their fleet that you allowed Legion to access. We have reached a consensus involving them and the creators. We wish to align ourselves with the collective known as the council and seek peace with the creators."

Shepard stared at the Geth for a long moment in shock.

"This is…unexpected." Shepard finally said.

"Not at all." The Collective responded. "We have analyzed all the available data Legion has collected. We are concerned for the Collective and our survival. Steps are being taken to protect ourselves from heretic infiltrators and the old machine invasion. Also, recent events involving yourself and the creator designated Tali have given us new information as to our creator's race. We have hundreds of colonies on numerous planets and moons in the Perseus Veil. The creator's home world has been abandoned by us for some time, as have most their colonies. We are prepared to reach a peace agreement with them and wish for you to be our representative along with the platform Legion. Given your standing in the creators' eyes we believe you will help us succeed."

"I am honored but I have to ask, how do I know this is not some plan to gain access to the Flotilla or to lure it into a trap?" Shepard asked. Legion was silent for a moment before picking up a blank data pad on the table. The pad clicked on and the screen began to rapidly fill with numbers and statistics. After a few moments Legion set it down.

"We have downloaded detailed information on our numbers, ships, and locations. As you will see Shepard Commander, our numbers alone on mobile platforms outnumber the human species five to one. Our ships also outnumber the Citadel & Alliance fleet as we know it by two to 1. If we wished to annihilate the creators, we would do so. As for learning the locations of the Flotilla, we will not maintain FLT communications to the Legion platform past this meeting. The Legion platform will be willing to be deactivated until it reactivated on the ship to speak with the creator leaders. Then it can be deactivated again until taken far from their location. We have also downloaded this agreement to the data pad with our signature as it were."

Shepard was quiet for a moment, thinking it over. He'd have to talk it over with Tali and contact the Quarian Admirals, but to have the Geth fleet on their side in the war would be a huge asset. Plus the Quarians could go home.

"While the Normandy is being restored I'll try and arrange meetings with the Quarian Admiralty board and the Council. I'll even help to try and convince them to accept but it will be their decision." Shepard answered. Legion nodded and stood. Shepard stood as well.

"We understand Shepard Commander. We have given the Legion platform specs and allowance to share our tech with you for your ship as a gift for your help. We believe humans shake hands to seal a deal?" Legion extended its hand. Shepard gave a grin and shook the Geth's hand.

"I hope this leads to peace between your people and others." Shepard said firmly. Legion nodded.

"As do we Commander. Disengaging link." Legion responded. Shepard released Legion's hand and there was a slight pause.

"FLT communications link to Legion has been severed. Restoring firewalls and resetting passwords and fail safes." EDI called out.

"Thanks EDI." Shepard called out as Legion began to move again.

"Shepard Commander." Legion said in its normal tone of voice. "We thank you for allowing us to speak with you again. We will now return to making repairs on the ship."

"Thank you for giving us this opportunity, Legion." Shepard called after the Geth as it left. Legion did not respond and quickly left the cabin. Shepard sighed and rubbed his eyes feeling more tired then ever.

"It's been a long damn day." Shepard muttered to himself. He glanced at the door before calling out. "Cabin door, lock!"

The door beeped before locking again. Shepard gave a weary sigh before stripping off his shirt and throwing himself onto his bed.

"Lights off!" He called, kicking his shoes off as the cabin went dark.

The next few days were going to be very, very long.

To be continued…