Prologue
Citadel:
"The paths are open. But you have to choose" The Catalyst said to a bleeding Commander Shepard. He thought about everything the AI had told him and the options it had presented. Destroy. Control. Synthesis. He had almost reached a decision and stepped forward.
"Shepard!" a voice buzzed over his earpiece.
"EDI? What are you doing here?" Shepard asked, wondering what she could be after right now.
"I've been listening to your conversation with the Catalyst AI. I have also been monitoring the Crucible from the Normandy. Shepard, the Catalyst is lying, the three options are a ruse to get rid of you!" she said
"Do not believe your construct, Shepard" the Catalyst replied, "it merely fears the Crucible's power. Now make your decision, human"
Shepard was suddenly unsure about the Catalysts intentions. But at the same time, he couldnt just abandon the Crucible after everything they had been through to get it here.
"Shepard, the Catalyst has taken control of the Crucible! you activate it and nothing will happen!" EDI responded through the comm.
He looked up at the Crucible, the various lights on the enormous machine were flickering. He pointed his gun at the image of the child.
"Why?" was his only word.
"Survival" it replied, but in a much deeper, booming voice reminiscent of a Reaper, "You would have destroyed us, we cannot allow that to happen."
"You bastard! I could have picked synthesis!"
"Synthesis is too unpredictable, even for us. You would never have chosen that when a chance for ultimate victory stood next to it. This Cycle has revealed that organics are too dangerous to evolve even this far. I have already devised a new, permanent solution"
"And that is?" Shepard asked
"Extermination" it retorted
"EDI, get me out of here!" Shepard barked into the comm.
"Roger that, commander"
"Shepard, be ready, we're coming in hot!" a familiar vooice radioed in
"Cortez? where?" Shepard looked up at the battle raging above
"You'll see me, I got a new shuttle!" and with that he flew in full-throttle, hitting the deck and skidding to a halt metres from Shepard. The doors opened and James and Ashley stepped out, fully armoured and carrying assault rifles.
"You look like shit, Loco!" James said
"Shepard, inside, quick!" Ash yelled as James held the Commander for support
Shepard limped into the shuttle as the Catalyst had a final thing to say
"Shepard" it said, causing James and Ash to point their rifles at it. "Regroup. Reload. Prepare. Wait. Fight. We will find you, your worlds, your armies, your children. We will show no mercy. No remorse. No regret. We will destroy you all."
Shepard only had one thing to say to this machine: "Fucking try it." The doors closed and the shuttle lifted away. As they cleared the Citadel Shepard looked out the window to see Reapers converging on the Crucible and opening fire, destroying months of resources and work.
"All Fleets, this is Admiral Hackett, abort the mission, I repeat, abandon Earth. We failed. Head through the Sol relay and scatter. Initiate Silent Contingency and await radio silence until further notice. We'll regroup, people. We'll beat them somehow. We'll continue the war..."