Kaidan had remained behind on the Normandy to prep the bomb and Ashley had gone with the salarians while the rest of them made their way to the facility.

Kirrahe's voice came over. "Comm check. Do you read me, Commander?"

"Loud and clear."

"Good. We'll start our push. We'll try to make it to the AA guns, but it might be up to you to finish the job. And Commander? If you see any way to undermine their defences, we could use the help."

"All right, people." Shepard hefted his rifle. "Lock and load."

"Tali, turret controls." Shepard tossed her one of the small explosive packs, then shifted position to snipe some of the oncoming geth.

The quarian set the charge, and then dove for cover. Wrex moved in and stomped, crushing the head of a half-destroyed geth still trying to get to its weapon.

"Communications disrupted." Tali got back to her feet and tossed off a salute.

"Then let's move forward," said Shepard.

He heard Ashley's voice on the comm. "We're getting pounded. Bunker up before the aircraft return!"

"Tali, with me. The rest of you, cover us." Shepard pointed. "Let's blow those refueling tanks before the aircraft take off again." He moved in, Tali on his heels.

"We've got access to base security." Garrus looked over the hacked console. "Should be able to cut alarms from here. Might even be able to trigger alarms on the far side of the base. It'll clear the guards out for us, but they might be too much for the salarians infiltration teams to handle."

"Just disable the alarms. We can handle any guards inside."

Garrus nodded. So far they were pretty unscathed, but from what they were hearing over the comms the salarians were taking casualties. The commander was more worried than he was letting on.

"Salarian prisoners?" Shepard frowned.

"The captain mentioned he lost then men." Liara nodded.

Shepard rubbed the back of his neck, and approached one of the cells. The salarian inside rose. "Well, you're not geth. And you're not wearing a lab coat. I guess I'm glad to see you. Lieutenant Ganto Imness of the Third Infiltration Regiment, captured during recon. I assume the fleet was called in to destroy the base?"

Shepard shook his head. "The transmission wasn't clear. The fleet is not coming."

The Lieutenant nodded. "I see. Then you must be the infiltration team. I know the captain. He will want this facility destroyed. My team was altered, indoctrinated. He knew about the breeding grounds. But the indoctrination is a greater threat, and far more horrifying. I watched good people reduced to mindless husks. There wasn't anything left. Others died during the experiments. I envy them."

"You know anything about the experiments they were conducting?" Shepard asked.

"They were studying indoctrination. Symptoms, progress. Saren uses it to control his people, but I don't think he fully understands it. I don't know much else. I just saw what it did to the others. Turned them into empty husks. I can't end up like that. Please… let me out!"

Shepard made his way to the controls. "I'm opening your cell, but you're on your own."

The Lieutenant nodded. "Don't look back and hope to outrun the blast, hmm? A better chance than I had before you showed up." The doors and opened and the Lieutenant exited his cell. "Thank you, human. And good luck. You'll need it."

Liara swallowed. "So, this isn't just a breeding ground for the krogan it's an indoctrination facility?"

"All the more reason to blow it up," said Shepard. "Let's move!"

The strange husk beings were all over the lab. The krogan in the tanks appeared to have some similar circuitry embedded in them. Wrex punched one of the tanks, but nodded to Shepard. Shepard returned the nod.

Then he stepped back and let Wrex deal with the scientist in charge.

"Don't shoot! Please, I just want to get out of here before it's too late." There was an asari cowering under a desk.

"I'm not going to hurt you. Who are you?"

She rose, and gestured at herself. "Rana Thanoptis, neurospecialist. But this job isn't worth dying over. Or worse. You think indoctrination only affects prisoners? Sooner or later, Saren will want to dissect my brain too!"

That was very much not helping her case. "I thought this was a breeding facility."

"Not this level. We're studying Sovereign's effect on organic minds. At least, that's what I assumed. Saren kept us in the dark as much as possible."

"You helped him and you don't even know why?" Garrus stared at her.

"I didn't have the option of negotiating. This position is a little more…" She shook her head. "Permanent than I'd expected. But I can help you. This elevator behind me goes to Saren's private lab. I can get you in." She swiped a card. "See? Full access. All of Saren's private files. Are we good? Can I go?"

"What were you studying here?"

"It's that ship, Sovereign. It emits some kind of…" She shrugged. "Signal. Undetectable, but it's there. I've seen the effects. Saren uses it to influence his followers, to control them. It's called indoctrination. Direct exposure to the signal turns you into a mindless slave, like the salarian test subjects. But there's collateral damage, too."

He asked her a few more questions, and noted that Liara were paying close attention to the answers. Though the idea that Saren might not be the one controlling the ship was… A bit more disturbing than he liked.

"I'm going to blow this place to hell and gone. If you want to make it out alive, you better start running."

She stared at him horrified. "What? You can't… but I'll never… ahh!"

She then ran like greased lightning.

Garrus smirked at Shepard. "You enjoyed that, commander."

"Commander, look over here. It's another beacon. Like the one on Eden Prime."

Shepard headed in the direction of Garrus's voice. Sure enough, there was another beacon. Glowing. Someone had clearly used it and he was willing to bet that it was Saren. He walked to the beacon, and touched the controls.

Images flooded into his head once more.

Liara quickly ran to his side, helping him back to his feet. She ran the medical scanner over him. "Commander?"

"I'm fine." Shepard rubbed the back of his neck. "I saw some more images and I think we found what we've been looking for. We'll sort this out later once we complete the mission."

Liara nodded.

They headed back up and saw a hologram of Sovereign hanging in the air. Wrex sighed. "I get the feeling something bad it about to happen."

"You too?" Shepard shook his head.

"You are not Saren." The voice came from the hologram.

"What is that?" Garrus frowned. "Some kind of VI interface?"

"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 stared.

"This 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 some Reaper ship Saren found." Shepard stared. "It's an actual Reaper!"

"Reaper? A label created by the Protheans to give voice to their destruction. In the end, what they choose to call us is irrelevant. We simply are."

Liara just stared at it. "The Protheans vanished 50,000 years ago. You couldn't have been there. It's impossible!"

"Organic life is nothing but a 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."

"There is an entire galaxy of races united and ready to face you." Shepard narrowed his eyes.

"Confidence born of ignorance. The cycle cannot be broken."

"Cycle? What cycle?" Garrus asked.

"The pattern has repeated itself more times than you can fathom. Organic civilizations rise, evolve, advance. And at 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."

Shepard frowned. "Why would you construct the mass relays, then leave them for someone else to find?"

"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 organics evolution. You exist because we allow it. And you end because we demand it."

"They're harvesting us!" Liara took a half step backward. "Letting us advance to the level they need, then wiping us out!"

Shepard tried to ask even more questions about the Reapers, but Sovereign just merely insulted them. Claiming that they exist for no other reason than to be wiped out, which didn't make a whole lot of sense.

"You're not even alive. Not really." Shepard shook his head. "You're just a machine. And machines can be broken!"

"Your words are as empty as your future. I am the vanguard of your destruction. This exchange is over."

And something exploded.

"Commander?" Joker's voice came over the comm. "We got trouble!"

He didn't know the half of it. "Hit me, Joker."

"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. It's coming your way, and it's coming hard! You need to wrap things up in there—fast!"

"This console has been disabled." Garrus gestured at the controls in front of them. "Orders, Commander?"

"Let's head to the breeding facility. Joker can pick us up after we set the nuke."

"Right, Commander. I'll meet you there. Joker out."

"Commander?" Liara glanced at him.

"We can discuss things back on the ship." Shepard gave her a reassuring nod. "However it appears that things are a lot more complicated than we initially thought."

"That's is an understatement, Commander," said Liara.

They fought their way through the breeding facility and eventually managed to locate the one deep viewpoint. After clearing the way by blasting tons of geth they managed to clear the site for the Normandy.

Joker brought the Normandy in, and Kadian and the crew began carrying the nuke off and putting it into place. Kaidan shook his head. "Bomb is in position, we're all set he—"

Ashley's voice came over the comm. "Commander, can you read me?"

"The nuke is almost ready. Get your ass to the rendezvous point, Williams!"

"Negative, Commander. The geth have us pinned down on the AA tower. We've taken heavy casualties. We'll never make the rendezvous in time."

"Get them out of there, Joker. Now!"

"Negative. It's too hot! Can't risk it. We'll hold them as long as we—"

"It's okay, Commander." Kaidan glanced up from where he was working on the nuke. "I need a couple of minutes to finish arming the bomb. Go get them and meet me back here."

Shepard nodded and looked to the others. "Up to the AA tower. Move!"

"You keep that nuke safe." He nodded to Kaidan and started moving.

They had to fight through more krogan and geth, but they were nothing more than steppingstones on a road.

"Reinforcements. We'd better hurry." Garrus gestured at the ship coming in.

"Heads up, L-T. We just spotted a troop ship headed to your location."

"It's already here. There's geth pouring out all over the bomb site."

"Can you hold them off?" Shepard glanced in the direction the ship had gone.

"There's too many. I don't think we can survive until you get here." Kaidan's voice was tight. "I'm activating the bomb."

"Alenko, what are you doing?" Shepard yelled.

"I'm just making sure this bomb goes off. No matter what." Kaidan was silent for a moment. "It's done, Commander. Go get Williams and get the hell out of here."

"Screw that! We can handle ourselves. Go back and get Alenko."

They were far closer to Ashley than they were to Kaidan and if they did get control of the AA guns then they will be able to escape the planet before the explosion. With a heavy heart he redrew his radio. "Williams, radio Joker and tell him to meet us on the AA tower."

It took Ashley a moment to respond. "Yes, Commander. I…"

"It's the right choice and you know it, Ash," Kaidan's voice said.

"I'm sorry, Kaidan. I had to make a choice."

"I understand, Commander. I don't regret a thing."

No. The regrets were going to be his.

They then ran towards the elevator as fast as they could and Shepard promised that he was in fact going to kill Saren when he saw him. They made it to the AA tower and found Ashley in a firefight with several salarians.

They soon joined with a combined firepower they began to push them back. Liara and Wrex use their biotics to push the geth over the edge of the tower. While Tali used her skills as a hacker to disorientate the geth making them vulnerable for his and Garrus' counter-attack.

For a moment, he thought they were clear. And then something exploded. It knocked Ashley and salarians off their feet. Shepard whirled to see Saren floating above them on a glider. It also turned out that he was a biotic and they quickly moved to recover. Saren jumped off his glider and Shepard began to fire several slugs from his pistol. It failed to get through Saren's barrier, and he ducked back.

It was then that he noticed something different about Saren from the last time he saw him on the hologram. He could have sworn that he saw metal on his skin and his eyes looked more robotic plus he had pipes sticking out.

"This has been an impressive diversion, Shepard. My geth were utterly convinced the salarians were the real threat. Of course, it was all for nothing. I can't let you disrupt what I have accomplished here. You can't possibly understand what's really at stake."

"Why are you doing this?" Shepard asked.

Originally Shepard believe that he was doing this for power to wipe out humanity, but he had a feeling that it was something more after seeing Sovereign.

"You've seen the vision from the beacons, Shepard. You, of all people, should understand what the Reapers are capable of. They cannot be stopped. Do not mire yourself in pointless revolt. Do not sacrifice everything for the sake of petty freedoms. The Protheans tried to fight, and they were utterly destroyed." Saren waved a hand. "Trillions dead. But what if they had bowed before the invaders? Would the Protheans still exist? Is submission not preferable to extinction?"

Shepard can believe he was hearing this. "Do you really believe the Reapers will let us live?"

"Now you see why I never came forward with this to the Council. We organics are driven by emotion instead of logic. We will fight even when we know we cannot win. But if we work with the Reapers—if we make ourselves useful—think of how many lives could be spared! Once I understood this, I joined Sovereign, though I was aware of the…" Saren shook his head. "Dangers. I had hoped this facility could protect me."

"You're afraid Sovereign is influencing you. You're afraid he's controlling your thoughts."

"I've studied the effects of indoctrination. The more control Sovereign exerts, the less capable the subject becomes. That is my saving grace. Sovereign needs me to find the Conduit. My mind is still my own…" Saren shrugged. "For now. But the transformation from ally to servant can be subtle. I will not let it happen to me."

"Tell me why Sovereign needs the Conduit," Shepard demanded. "Tell me what it is. Maybe we can find a way to stop them."

"The Conduit is the key to your destruction and my salvation. Sovereign needs my help to find it. That is the only reason I have not been indoctrinated."

Shepard shook his head. "Sovereign's manipulating you and you don't even know it! You're already under its power!"

"No! Sovereign needs me. If I find the Conduit, I've been promised a reprieve from the inevitable. This is my only hope."

"Together we can take down Sovereign," said Shepard firmly. "We don't have to submit to the Reapers. We can beat them!"

"I no longer believe that, Shepard. The visions cannot be denied. The Reapers are too powerful. The only hope is to join with them. Sovereign is a machine. It thinks like a machine. If I can prove my value, I become a resource worth maintaining. There is no other logical conclusion!"

Shepard can believe his ears, he was indeed a traitor, but not to the Council but to the galaxy. "You were a Spectre. You were sworn to protect the galaxy. Then you broke that vow to save yourself!"

"I'm not doing this for myself! Don't you see? Sovereign will succeed. It is inevitable. My way is the only way any of us will survive! I'm forging an alliance between us and the Reapers. Between organics and machines. And in doing so, I will save more lives than have ever existed. But you would undo my work. You would doom our entire civilization to complete annihilation. And for that, you must die."

Shepard came up shooting.

Saren threw a grenade, and the shockwave knocked him off his feet. Worse, it knocked his rifle out of his hands and sent it into the water.

Before he could find it, Saren grabbed him, lifting him by the throat and dragged into the edge of the platform. Something else exploded, and Saren turned towards it. Taking advantage of this distraction he punched the turian in the face, and they both fell.

Shepard grabbed his sidearm again, but Saren was already back within range of his glider's shields. Alarms started going off. He looked around for his team.

Wrex was lifting a piece of rubble while Tali pulled Garrus out from under it. Liara moved towards Ashley, who was holding her ribs and apparently unable to stand. The Salarians were on their backs with holes in their chests. Shepard went to pull Ashley to His feet.

The Normandy landed, and they stared moving towards it. Ashley stumbled and nearly fell again. Shepard caught hymn, then slung her over her shoulder and carried her into the ship. As soon as they were on board, he yelled for Joker to get them moving.

Kaidan meanwhile was heavily injured in the rest of his men were dead. He was leaning against the nuke trying to protect it long enough for the Normandy to escape. The geth were about to overwhelm him and that's when he noticed the Normandy flying past.

"Good luck, Shepard," he said as he continued to fire upon the geth.

On the Normandy Shepard was looking at the window at Virmire as they had just escaped the atmosphere.

"Everybody hang on!" Joker's voice came back over the comm.

Shepard watched as a huge explosion appeared and he closed his eyes knowing that he just lost a good friend.

"Goodbye friend," he said saluting.