As the group moved a couple of rooms further in, taking a couple of geth out on the way, they found an asari cowering below a desk. Fluttershy immediately lit up her wings but was blocked by Garrus as he quickly jumped between the pegasus and the asari.
“Don’t shoot! Please, I just want to get out of here before it’s too late!” she plead, Shepard had his weapon raised at the asari as he couldn’t afford to be caught off guard.
“Identify yourself,” he calmly stated but somehow that only made him sound even more intimidating.
“Rana Thanoptis, neuro specialist. This job isn’t worth dying over… or worse. Do you think the prisoners are the only ones affected by the indoctrination? Eventually, Saren will want to dissect my brain too!” she said very much in a panic. Shepard looked over at Fluttershy who no longer had her wings lit up in a biotic aura.
“Can you try to check if she isn’t indoctrinated?” the Commander asked, Fluttershy nodded and stepped forward, unleashing the stare at the asari. The pegasus still felt the strange disturbance in the asari’s brain but the moment she touched the contaminated spots of her psyche they withered and disappeared.
“She’s good, Commander,” Fluttershy answered as she released the stare, the asari gasping for air after having been exposed to the technique.
“I thought this was a breeding facility?” Shepard asked while Rana wearily glanced at the pegasus who was glaring at her.
“Not this level, here we were studying the effects of Sovereign on organic minds. Saren tried to keep us in the dark but that’s hard if you’re the one studying its effects,” She answered hastily, “I didn’t want to stay, but it wasn’t as if I could just leave. The position was a little more permanent than expected, but I can help you. The elevator behind me goes directly to Saren’s personal lab, and I can get you in,” she explained as she walked to a console and tapped a few commands, the door to the elevator opening. “I also gave you full access to Saren’s files. Please, can you let me go?”
Shepard looked troubled at the asari, “I don’t trust you, but if Fluttershy says you are good then I’ll trust her judgment. I suggest you start running because I’m going to blow this place to hell.”
“W-What! But… you can’t… I’ll never make it!” The asari panicked and rushed past the group to get herself to safety. Shepard sighed as the door closed behind them again.
“Come on, we need to figure out what Saren was doing in his personal lab,” the Commander stated and the group stepped into the now unlocked elevator and went up. As they stepped out of the elevator the group froze as they saw what stood in the lab.
“Holy crap, is that a prothean beacon?!” Garrus said as he was the first to come out of his stupor.
“Yes it is,” Shepard said as he immediately walked up to the device which seemed to activate in the Commander’s presence. Fluttershy tried to retreat from the device as she suddenly felt pressure building in her mind but was too slow.
The vision she had gotten from Shepard in the Normandy flashed through her mind again, only this time it was clear as day. The entire event only took a few seconds but by the time it was done both Shepard and Fluttershy were weakly trying to get up again.
“You two good?” Wrex asked as the human and pegasus found their feet again.
“Yeah, let’s get out of here. We got what we needed,” Shepard stated as he took the lead towards the exit. He didn’t get far as a hologram of the ship that had attacked the colony on Eden Prime came to life.
“You are not Saren,” It stated in a reverberating mechanical voice.
“Is that a VI interface?” Fluttershy asked, a shiver going up her spine
“Rudimentary creatures of blood and flesh. You touch my mind, fumbling in ignorance, incapable of understanding.”
“I don’t think this is a VI...” Garrus said, answering Fluttershy’s question.
“There is a realm of existence so far beyond your own you cannot even imagine it. I am beyond your comprehension. I am Sovereign!”
“Sovereign isn’t just a ship, it’s a reaper!” Fluttershy said as she connected the dots.
“Reaper? A label created by the protheans and your species to give voice to their destruction. In the end, what they choose to call us is irrelevant. We simply are.”
“M-my species?!” Fluttershy said alarmed, had ponies faced these things before? “How could you have even been there? That was fifty-thousand years ago!”
“Organic life is nothing but genetic mutation, an accident. Your lives are measured in years and decades. You wither and die. We are eternal, the pinnacle of evolution and existence. Before us, you are nothing. Your extinction is inevitable. We are the end of everything.”
“You will face a united galaxy when you come! We won't let you destroy anyone!” Shepard shouted at the construct in rage, not that that it seemed to faze it in any way.
“Confidence born of ignorance, the cycle cannot be broken.”
This time it was Garrus who first spoke, “Cycle? What cycle?”
“The pattern has repeated itself more times than you can fathom. Organic civilizations rise, evolve, advance. And in the apex of their glory, they are extinguished. The protheans were not the first. They did not create the Citadel. They did not forge the mass relays. They merely found them, the legacy of my kind.”
“Why would you construct the mass relays and then leave them?” Shepard asked the reaper who answered in kind.
“Your civilization is based on the technology of the mass relays, our technology. By using it your society develops along the paths we desire. We impose order on the chaos of organic evolution. You exist because we allow it. And you will end because we demand it.”
“We will not allow it! We’ll find a way to stop you!” Fluttershy shouted at the hologram in rage as she flew up into a hover.
“Your words are as empty as your future. I am the vanguard of your destruction. Our numbers will darken the skies and extinguish the light of your civilizations. This exchange is over.” The glass window panes of the lab exploded inwards as the hologram of the reaper vanished, Joker’s voice coming over the radio almost immediately after.
“Commander, we’ve got problems. That ship sovereign? It’s moving. I don’t know what you did down there but that thing just pulled a turn that would shear any of our ships in half,” The pilot reported. “It’s coming your way and it’s coming hard! You need to wrap things up in there—Fast!”
“Fuck,” Shepard swore as he started running to the elevator. “We need to set that nuke and get out of here. Now!” He shouted as everyone got into the elevator. With time running out on them the group didn’t bother with overly clever tactics and charged in the direction of the base’s AA tower that was stopping the Normandy from approaching. Their shields took a beating from all the various resistance along the way, but nothing had yet to down them completely.
“Fluttershy, get up there and Disable that AA gun!” Shepard shouted as he cleared the last of the geth out from below the air defence emplacement. The pegasus flew up ahead and found the appropriate console, disabled it, and shot it a couple of times for good measure.
“Turret is down, Commander!” She called out to the squad that was just coming up the ramp, an elevator at the back wall came to life and a small group of signatures appeared on the group’s motion tracker.
“Enemy units in the elevator, take aim!” Shepard said as he himself also raised his weapon. The moment the doors opened, everyone let loose a barrage of fire, the few geth troopers in the elevator being destroyed within seconds. “Nicely done, let's get topside to secure the bomb site.”
Taking the same elevator the geth unit had used, the group found themselves at the site that had been designated as the place where the nuke had to be detonated. The STG captain soon after had reported that they had taken down their AA tower as well, clearing the path for the Normandy to approach. Joker didn’t waste any time bringing the frigate in close and dropping its lethal payload off. Ashley and a few other crew members carrying the bomb out of the Normandy.
“Bomb is in position, we’re all set here!” Ashley reported, but was interrupted by a radio transmission from the Captain Kirrahe and Kaidan.
“Commander, do you read?” The STG captain asked, gunfire in the background of the transmission.
“Five by five. Get your team to the rendezvous point, Captain. The nuke is set and ready!” Shepard warned the remains of the assault team.
“Negative, Commander. The geth have us pinned down on the AA tower. We’ve taken heavy casualties!” Kirrahe responded. Shepard swore and signaled the group to follow.
“Hold on, Captain. We’re coming!” he radioed to the assault team before turning to Ashley. “Get the nuke ready! I’ll come pick you up after we’ve gotten the salarian team!”
“Yes, sir!” Ashley shouted back at the Commander and quickly continued working on arming the nuke. Fluttershy followed Shepard as the Commander made a sprint to the other AA tower where the assault team was held up, on the way there they faced heavy krogan resistance, but that didn’t stop them from making slow progress towards the salarian strike team.
At about the halfway point between the AA tower and the bomb site a geth troop transport flew over and hovered above the latter location, Ashley opening a comm line. “The Geth just dropped reinforcements all over the bomb site! There’s too many. I’m activating the nuke!” she shouted.
“What the hell are you doing, Chief!” Shepard shouted back, calling Ashley by her rank.
“I’m making sure this bomb goes off no matter what! There, it’s done. Go get the Lieutenant, Commander!” Ashley said, something Kaidan didn’t take too kindly too.
“Belay that! We can handle ourselves. Go and get Williams!” He called out. Shepard stood still and didn’t look like he could make a decision who to pick. Only one could be picked up, which meant the death of the other.
Fluttershy didn’t envy the Commander’s position. If he left Ashley there would be a small chance the bomb wouldn’t go off, while if he left Kaidan he would also leave the STG team and open the possibility that the AA gun came back online.
But Shepard’s indecisiveness was costing them precious time. He needed a nudge in one direction or the other.
1. Encourage Shepard to go to Kaidan
2. Encourage Shepard to go back to Ashley