[Use the Stare in an attempt to purge the indoctrination] 93%
Fluttershy had no doubt within her mind as to what she needed to do. Back on Virmire, she had figured out that the Stare was able to purge the reapers’ indoctrination from the minds of its victims, as proven by the captured STG operative and the asari scientist. Last time when she had tried it on Saren, it had backfired on her, though it now seemed that hadn't been a complete waste of time.
The pegasus steeled her mind and jumped out of her cover, her eyes focusing on Saren's. To the others surrounding her it was as if gravity had changed direction, like everything suddenly centered around Fluttershy. Only for it to stop seconds later and Saren to fall unconscious.
But to the pegasus, these few seconds felt much longer. As her mind connected to the turian's she was immediately assaulted by the black corruption that was clouding his mental processes. Except where she had been utterly unprepared before, now her mental defenses held strong, the black tendrils chipping at Fluttershy's defenses but never breaching them while the pegasus went to work purging the taint from Saren's mind.
The deep-rooted corruption fought with all its might to stay attached to the turian Specter's consciousness, clinging on to it for as long as possible, but it was all for naught. Once it seemed to realize it was fighting a losing battle it changed its focus in on itself, trying to destroy as much of Saren's mind as possible.
Fluttershy abided none of it as without the tendrils slashing at her own mind she could focus on keeping his safe. It took an eternity longer before the final wisps of darkness were at last destroyed, leaving the badly mauled—but untainted—consciousness of Saren…
…and it was failing.
The damage done was far too severe for the healthy portions of his mind to fix and collapsed into the voids that the corruption had left when it was purged.
Nonononnono, NOT now, not after all the effort I went through to try and save him! Think Fluttershy, how do you stop his mind from degrading further?
The answer to her question came to her almost immediately after thinking it up.
You fill the holes!
Increasing the power of the Stare a bit, Fluttershy tried something new. She placed her power into Saren's mind, and instead of using it to push or pull on strings of intellect, she simply let it go.. Pale blue glowing energy immediately filled the holes, acting as scaffolding that kept the rest of the turian's consciousness in place. Feeling her energy reserves almost completely drained, Fluttershy cut off the flow of energy to the Stare and fell to her knees while Saren simultaneously fell unconscious. The turian fell off of his hovering platform, through a glass window, and into a garden that lay below the audience platform.
Shepard didn't waste a moment in sprinting towards the master control unit—the large holographic interface Saren had used to give Sovereign control of the Citadel's systems—and ran the program Vigil had given to him, leaving Garrus to check up on Fluttershy who was trying to get back up on her legs.
Tali had run up to the control panel as well and started typing in commands too. The two of them managed to get the Citadel arms open along with establishing a line of communication with any friendly forces in the area.
"…The Destiny Ascension. Main drives down and kinetic barriers at sixty percent. The Council is on board. I repeat, the Council is on board!" A distress call immediately sounded from the speakers as Shepard tuned into the local battlenet.
"Normandy to the Citadel, do you read? Please tell me that's you, Commander," Joker called out as well.
"I'm here, Joker. What's your status?" Shepard immediately asked, wanting to know what the status of the surrounding fleet now they had a shot at Sovereign.
"I'm sitting here in the Andura sector with the entire Arcturus fleet. We caught the distress call, commander. We can save the Ascension, just unlock the relays around the Citadel and we'll send the cavalry in!" Joker reported. Wrex huffed as he heard the proposal.
"You'd sacrifice human lives to save the Council? What have they ever done for you?" he asked skeptically. "You should hold them back until the Citadel's arms have fully opened up."
Does Shepard open the relays around the Citadel? Yes
"I can't, Wrex. Even though they've been in my way the entire time, if I let them die now, that'll create resentment towards humans which will make cooperation harder. Something we can't have if we are to oppose the Reapers," Shepard explained as he typed the necessary commands into the console. "Opening the relays now, Joker. Save the Ascension!"
The console screen immediately showed dozens of new contacts entering the space around the Citadel and engaging geth ships, the heightening fight costing the geth many ships and the Alliance a few as well. Knowing that they couldn't do anything about the space battle outside, Shepard turned his attention to Saren and then Fluttershy.
"Is he alive?" the commander asked, receiving an unsure nod from Fluttershy.
"He should be, but I'm not sure if he'll wake up."
"Garrus, take Fluttershy and check it out. If he's alive, make sure he can't harm you if he comes to," Shepard ordered. Fluttershy, having regained some of her energy, opened her wings and slowly glided down into the garden below while Garrus made a jump down. Fluttershy used her omni-tool to check on the turian’s vital signs, finding a consistent heart rate, something she was thankful for.
The tower suddenly trembled as the Citadel's arms had opened far enough for the Alliance fleet to open fire on Sovereign, the explosions from the shells violently impacting on the reaper's hull.
What the team in the tower couldn't yet see was the red lightning forming on the hull of the reaper that was slowly arcing down towards the tower. Fluttershy was about to call out to Shepard that Saren was alive for the moment when the lightning entered the chamber.
Without warning, it impacted Fluttershy, sending waves of agony through the pegasus' body. Her scream piercing the air as the lighting burned her fur and skin beneath through her armor.
“You persist too long after your own defeat.” Fluttershy couldn't identify if the voice came from inside her mind or from outside of it. She really could only focus on the crippling pain the lightning was inflicting on her body. “The cycle is inevitable, you cannot win.”
Images started flashing through Fluttershy's mind. Cities she had never seen and strange starships that didn't look like anything the current races possessed. But what was most remarkable was that ponies walked through the streets and manned the ships, peaceful and joyfully speaking to each other…
…Then hundreds of reapers, just like Sovereign, descended on the planet, firing their lasers at anything and everything that moved. Taking down buildings and starships alike, only losing a couple of their own numbers in the process.
“We shall be your downfall, just as we were before.”
Fluttershy gritted her teeth as she tried fighting the lightning that still bounced around her body.
"No."
The statement was resolute. The images that were being implanted into her mind stopped as Fluttershy forced memories of her own to the forefront. Fighting Nightmare moon, facing a dragon, re-sealing Discord in stone, all tasks that any sane pony would deem impossible.
"Me and my friends faced impossible tasks before, and now my new friends face another one. You might say that this is all for naught, but we'll find a way to stop you. Your cruel acts have gone on for long enough!" With her last statement Fluttershy felt herself filling up with new energy, the same energy she had been filled with when she had faced Nightmare Moon and Discord. Opening her wings wide released streams of blue lightning that, whenever it touched its red counterpart, dissipated it.
As the final bits of lighting faded away Fluttershy collapsed to the ground, her body completely spent from purging Saren's mind and taking on Sovereign in a battle of wills. She still remained conscious—barely—and was in no state for any action as the smell of burned fur reached her nose from beneath the armor.
"FLUTTERSHY!" Garrus shouted, sitting beside the fallen pegasus.
"G-Garrus, I feel cold," she whimpered as the turian checked her, his omni-tool warning him of the burns Fluttershy had received.
"Shhh, it's all right. You'll be fine," he said as he held Fluttershy close.
Outside, Sovereign had let go of the tower and helplessly drifted away from it, all of its systems offline.
"Its shields are down, now's our chance!" Joker's voice boomed from the speakers around the chamber.
"Hit it with everything we've got," Fleet Admiral Steven Hackett immediately ordered. Through the window outside the team could see how the helpless reaper was being pummeled, armor that had previously been protected by strong shields peeled off like it was nothing. Chunks of reaper were flying everywhere, and the barrage was not intending to show it any quarter.
But the killing blow did not come until the Normandy made an attack run, the nimble scout ship using a disruptor torpedo to completely pierce the monstrous starship and set off many internal explosions. The cheer of the group was short lived as one of the pieces of debris from the reaper flew directly towards the tower.
Garrus immediately took action and carried Fluttershy to one of the walls, hoping that it would shield them from the flying chunk of spaceship. Something it managed as the wreckage crashed through the large window and smashed down in the council chamber, burying the two of them below a heap of scrap metal.
This was also when Fluttershy finally let her consciousness slip away from her, all the pain coursing through her body simply becoming too much. But she had done what she had set out to do. Sovereign was gone. Although the greater threat still loomed, she could rest now.