Shepard woke up with a sharp pain in his head probably from the Reaper beam. But where was he? It looked like a fighter, possibly Cerberus. Why was he in a Cerberus Fighter? How did he get here? He began looking out the window to discover his location. He was in orbit around the moon. He turned off the auto-pilot and began towards Earth.
My God! The Citadel is gone! It had exploded. Shepard assumed that meant it worked but who triggered the crucible? Anderson? He had to find Tali. He began maneuvering towards the mass relay.
The Relay had also been destroyed and a bright green aura. Did this happen to all of the Relays? Where would he go? Shepard had never been so confused in his life. He turned back to Earth which was also covered with the same green aura. The next thing he noticed was that the reapers were not destroyed. The reapers were retreating. Why were they retreating and why were we letting them?
Maybe communications are up. Shepard began to hail the field base when he receives a repeated transmission being sent galaxy wide.
"Do not attack the Reapers! We are one now. Organic is synthetic and synthetics is organic. We are one!" once this transmission had finished it repeated over and over again. It also transmitted coordinates to a recovery space station. Shepard set a bearing for the station.
When he reached the general vicinity of the station he attempted to hail their comm channels.
"This is Commander Shepard, Alliance forces, requesting dry dock." he said.
"Stop hailing this channel it is cruel to remind the cadets of what happened." said the woman at the comm.
"That's why I'm here. Someone sent me into orbit around the moon in a Cerberus fighter. What happened? Why are the Reapers retreating?" he sked.
"Sir please move along to the rescue docking area. If you are injured I will send assistance as soon as possible. Goodbye." the woman lost the channel. Shepard was beginning to get frustrated.
He pulled into the citizen docking bay. The guards approached him immediately obviously having him tagged as Cerberus. He told them that he was Commander Shepard Alliance Navy. The guards gave some generic speech discrediting his claim as if many people had claimed it already.
"Who is your commanding officer?" Shepard asked.
"Commander Bailey leads the C-Sec at the command center on this station." said one of the guards. Shepard looked at them closely and noticed that they to were covered with the green aura just as earth and the wreckage of the Citadel and the Mass Relay were. He also noticed that their eyes were a bright green. He looked at his arms and noticed that they were not covered by the green aura.
Shepard made his way towards Baileys office on the station. He wondered how long he'd been unconscious. Where was Tali? He hated the feeling of not knowing what was going on, it was worse than waking up on the Cerberus station after they had revived him.
Once he arrived at Baileys office, he noticed a long line of military and political leaders waiting to enter. He began to walk towards the front of the line when Councilor Valern grabbed him.
"Hey, your going to have to wait in line like the rest of us pal.-" When Shepard turned around the Councilor silenced and stared in fear. "Nevermind, you go right on ahead." Shepard walked up to the door. He could here Bailey yelling from the other side.
"We aren't sure what exactly is going on right now! You need to calm down and find boarding until we have further news and the mass relays are up and running again." he yelled at his client. The man stomped towards the door leaving it open for him to enter. "Nita send in my next appointmen- never mind, hold my calls and cancel all my appointments for the next hour." Bailey was also staring at him as Valern was.
"Hey Bailey, how have you been?" Shepard asked. Bailey continued to stare at him. His eyes were struck with fear, wonder, and relief.
"Well where the hell have you been?" asked Bailey. His eyes began to calm and turned into more anger than fear.
"I have been in orbit around the moon in a Cerberus fighter for God knows how long. I'd like some answers." Shepard said, releasing a bit of his frustration out on Bailey which he felt bad for doing.
"Oh yeah, you probably are very confused right now. I mean technically you're dead...again. Someone and Anderson went up to the Citadel to fire the crucible. The Illusive man attempted to stop them and killed Anderson in the process but Shepard killed him.
After that we don't really know what happened up on the citadel, but once the crucible fired it shot a green beam out from it towards Earth and spread all throughout the galaxy using the Mass relays. For awhile we weren't a hundred percent sure what happened. Whatever it was it had affected both Organics and Synthetics. We think what has happened is that organics now have the strength and intelligence of synthetics and synthetics have a full understanding of organics. The reapers understand our needs and desires now and have helped us. We have full of reaper technology and the history of the past civilizations." Bailey explained in somewhat confusing detail.
Shepard was skeptical and wondered if it was truly over. The reapers were the greatest threat in the galaxy, possibly the Univererse, and now they're collaborating? It seems unlikely.
"How long has it been since the Reapers surrendered?" Shepard asked. "About a week. You were probably knocked unconscious by a reaper beam and somebody pulled you over to that Cerberus fighter you came here in. My guess was it was the same person that went up there to take your place on the Ciadel. You were probably affected by the beam in a way others wouldn't be. Most would die, you were probably knocked unconcious by it for a long period of time." Bailey explained. This was hard to believe. He had been presumed dead for a week. Somebody gave his life so he could survive. Who would do that for him? "Is everybody from the Normandy okay?" Shepard asked sincerely. "Everybody on the Normandy's crew survived. Well, everyone except for you. They just held a memorial service, Tali put your name up on the Normandy memorial wall." Bailey answered.
"Where are they?" Shepard asked. The crew had broken up once again. The Normandy was put in dry dock to be handed over to the command of S.P.E.C.T.R.E. Luitenant-Commander Ashley Williams, who was currently on shore leave on the Refugee Space Station along with Liara T'soni.
Shepard would gather his crew again and submit himself for orders. He was still a council S.P.E.C.T.R.E. and had to follow the commands of the Alliance. He failed his mission even though it was completed and he had to make up for his failure.