A big part of this chapter is Vigil being a chatter bug. I swear I already cut half of what he said but he still keeps on monologing in this chapter like a failed Shakespearean actor.
But what he says is just so important to the story of Mass Effect, this is actually the one place where we get an explanation, that I felt I had to keep it in here.

Next chapter will be less chatter and more action, I promise.

Shepard drove slowly and carefully, despite the urgency. The tunnel was wide and so high that the upper ceiling disappeared in fog. Everything was covered with thick roots and vines, making the ground uneven. Dust particles drifted in front of them, swirling away in the airflow from the Mako.

"I never dreamed I would discover anything like this," Liara said quietly, staring out the windows. "I've studied the protheans all my life but this is more than I ever hoped for."

"What are those things?" Shepard wondered aloud about circular containers protruding from the walls.

"Cryopods, maybe," Liara said. "They must have thought they could stay in stasis until the Reapers came back. This bunker was possibly the last refuge of their whole species."

"You mean there could still be frozen protheans in there?"

"I'm not getting any energy readings in here, from anywhere," Garrus said. "This building is dead, I don't think the cryopods still work."

"There must be thousands of these pods," Langenfeld said.

Liara sighed. "They were still hopeful. Even in their defeat, they hoped to survive to fight the Reapers again."

Shepard scrunched up her nose. "Sounds either arrogant or delusionary."

"Yeah," Wrex grunted. "They lost the war once and thought they could win it on second try?"

They drove on in grim silence. Shepard avoided the roots, a thick as the Mako's tires in some cases, as best as she could but they still almost tipped over on more than one occasion.

"Commander! Vehicle up ahead."

"What kind?"

"About the size of the Mako. Could be Saren's." Madhav was sticking his head out of a side window and increased the amplification of his omni-tool with a special tool-attachment.

A grin spread on Shepard's face. "Please tell me he was stuck down here the whole time too."

Madhav came back inside and closed the window against the stale, damp air.

"It doesn't look like the TAP tank has been damaged. Something must have kept them here." Garrus scanned for energy signatures and obstacles ahead of them but there was nothing to find. Nothing that could have stopped a Turian All Purpose tank.

"That's the best news I heard all week. Saren's head-start is much smaller than I expected, " Shepard said and sped up the Mako.

Excitement churned in Garrus' gizzard, finally they were making progress. He could almost feel that traitor under his talons. It was about time.

He kept scanning, trying to get a reading on the TAP tank. As he stared at the data, something flickered in the background of the image.

"Stop!" he yelled.

Shepard reacted instantly, slamming the breaks and making everyone happy to be strapped in, as the Mako skidded over the wet surface. They came to a sudden stop, the Mako crashing into an invisible barrier and the vehicle shut down.

Not a single light was on on the dashboard and the lack of sound from the engine made every noise louder than a gunshot. Shepard turned around and made one small movement with her hand and the marines nodded in unison. No words were spoken, only the sound of scraping armor, charging shields and weapons being readied could be heard.

They exited the Mako one by one, leaving only two marines as guards behind. A barrier glowed golden in front of the Mako, sealing the tunnel off.

"Is this a trap by Saren?" Shepard asked.

Garrus and Tali both scanned the barrier, trying to trace it to the emitters. "It does not look turian," he said.

"Agreed and it's not geth either," Tali said. "But it looks — "

"It looks prothean," Liara said with conviction. "As little as we know about prothean technology, this mass effect field looks like the ones we have encountered with the security fields of this place."

"But..." Shepard looked around at the pods sticking out of the walls, overgrown by thick roots and vines. "But we do agree that the protheans are all dead in here?"

"It must be another automatic system."

"And it wants us to go in there." Shepard pointed to an opening in the wall. It was the only gap in the solid wall that stretched up into the permanent fog of Ilos. It was lined with vines and low plants seemed to spill from it like an unfinished welcome carpet.

Garrus scanned the area but all he got was a faint image of movement on the other side of the shield. The opening led to an elevator and he scanned again, trying to find a trap, a sign, anything that he could prepare for. But Ilos kept its secrets.

Shepard ordered the marines to stay behind and entered the elevator with Wrex, Garrus, Tali and Liara.

"I hope, when all this is over," Liara said, "I can come back and really study all of this. Just imagine what kind of knowledge we could gain."

"If the reapers didn't destroy everything," Shepard said.

"Ilos seems to have escaped the reaper threat." Liara looked out a window on the side of the cabin with a wistful sigh. They could see the underlying structure of the complex, huge support beams, tunnels and ramps connecting to various structures. These underground systems were gigantic, they had obviously only seen a fraction so far.

The elevator opened to a hollow in the giant cavern with a bridge leading into it that seemed to go nowhere. It looked rather pointless to have an elevator stop here. But as they walked over the bridge, a holographic image flickered to life at the end.

Shepard raised her pistol. "If that is another one of those 'rudimentary sacks of liquid and flesh' things. I'm just gonna shoot it. I don't have time for this shit."

Garrus couldn't agree more. He considered this whole stop a waste of precious time, now that they knew that Saren hadn't gotten far either. This could be their only chance at stopping Saren's plans, whatever they were.

As they came closer to the hologram, it looked like a representation in golden light of the spinning rings in a mass effect relay. But it flickered and distortions rippled over it.

"Looks like some kind of VI interface," Tali said as she scanned it, "but it's badly damaged."

"You are not Prothean," the hologram spoke in a pleasant voice. Shepard slowly lowered her pistol.

"But you are not machine, either," the VI continued. "This eventuality was one of many that was anticipated. This is why we sent our warning through the beacons. I do not sense the taint of indoctrination upon any of you. Unlike the other that passed recently. Perhaps there is still hope."

Shepard holstered her pistol and stepped closer. "So it is real? The indoctrination is used on purpose, as a method of warfare?" "Your nomenclature is abt. I have been monitoring your communications since you arrived at this facility and have analysed your descriptions."

Garrus stepped forward. "That's why we understand you?"

"Yes, I have translated my output into a format you will comprehend."

"Who are you?" Shepard asked. "My name is Vigil. I am an advanced non-organic analysis system with personality imprints from Ksad Ishan, chief overseer of the Ilos research facility. You are safe here, for the moment. But that is likely to change. Soon, nowhere will be safe."

"Why are we here? Why did the beacons and the visions draw us here?"

"You must break a cycle that has continues for millions of years. But to stop it, you must understand or you will make the same mistakes we did."

Vigil continued to explain how the protheans had just been one civilisation in an endless cycle of civilisations that had been wiped out by the reapers. Every civilisation at some point discovered the mass effect relays and the Citadel and built their society around them.

"But the Citadel is a trap. The station is actually an enormous mass relay," Vigil said. "One that links to dark space, the empty void beyond the galaxy's horizon. When the Citadel relay is activated, the Reapers will pour through from dark space. And all you know will be destroyed."

Shepard looked sceptical. "Nobody ever noticed that the Citadel is a relay?"

"The Reapers are careful to keep the greatest secrets of the Citadel hidden. That is why they created a species of seemingly benign organic caretakers. The keepers maintain the station's most basic functions."

Wrex snorted. "With the keepers, nobody needed to understand completely how everything works."

"But," Shepard looked at Wrex in confusion, "was nobody ever curious? You've been using the relays for centuries. I mean, nobody ever wanted to take things apart to see how they work?"

Wrex chuckled at that. "If humans had been the ones to discover the Citadel, I bet they would have crawled all the way down into the deepest tunnels to look for the bolts that held everything together. Unfortunately, it was only asari."

Liara's head whipped around. "What do you mean unfortunately?"

"Well, they just accepted it, didn't they? The asari discovered the Citadel, and just took it as given. Said hello to the keepers and invited other species to come." Wrex shrugged. "Not that they allowed them to participate on that governing idea for the longest time, but they sure could come and be impressed by the technology."

"Enough, Wrex," Shepard said.

Liara looked furious but didn't say anything.

Vigil's hologram blinked and then he continued. "Reliance on the keepers ensures no other species will ever discover the Citadel's true nature. Not until the relay is activated and the Reapers invade."

"And then the Reapers can wipe out the Citadel and the entire Citadel fleet in a single surprise attack," Garrus said. "That was our fate. Our leaders were dead before we even realized we were under attack. The Reapers seized control of the Citadel and through it, the mass relays. Communications and transportation across our empire were crippled. Over the next decades, the Reapers systematically obliterated our people. World by world, system by system, they methodically wiped us out."

"And the reapers live in dark space, just waiting?" Shepard wondered, more to herself but Vigil answered anyway.

"We have only theories. The researchers here came to believe the Reapers enter prolonged states of inactivity to conserve energy. This allows them to survive the thousands and thousands of years it takes for organic civilization to rebuild itself."

"But what is the point of that? Why wait for civilisations to grow, only to wipe them out?"

"The Reapers are alien, unknowable." More distortions rippled over the VI interface. "Perhaps they need slaves or resources. More likely, they are driven by motives and goals organic beings cannot hope to comprehend. In the end what does it matter? Your survival depends on stopping them, not in understanding them."

Shepard shook her head. "Yeah, you clearly don't know much about us. We want to understand everything."

"I'm afraid you won't have time for that." The interface now flickered randomly. "Your enemy has a single goal: the extinction of all advanced organic life. That's what happened to us. Through the Citadel, the Reapers had access to all our records, maps, census data. Information is power, and they knew everything about us.

"Their fleets advanced across every settled region of the galaxy. Some worlds were utterly destroyed. Others were conquered, their populations enslaved. Theses indoctrinated servants became sleeper agents under Reaper control. Taken in as refugees by other Protheans, they betrayed them to the machines. Within a few centuries, the Reapers had killed or enslaved every Prothean in the galaxy. They were relentless, brutal and absolutely thorough.

"Our worlds were stripped bare, harvested by the indoctrinated slaves. Everything of value-all resources, all technology-was taken. Certain that all advanced organic life had been extinguished, the Reaper retreated back through the Citadel relay into dark space, sealing it behind them. All evidence of the Reaper invasion had been wiped away. Only their indoctrinated slaves were left behind, abandoned. Mindless husks no longer capable of independent thought, the indoctrinated soon starved or died of exposure. The genocide of the Protheans was complete."

Shepard squared her shoulders, looking ready to take up anybody in a fight. "How do we stop them?"

"The Conduit is the key. Before the Reapers attacked, we Protheans were on the cusp of unlocking the mysteries behind the mass relay technology. Ilos was a top secret facility. Here, researches worked to create a small-scale version of mass relay. One that linked directly to the Citadel: the hub of the relay network. The Conduit is not a weapon. It's a backdoor onto the Citadel."

"Did you use it?" Garrus asked.

"Yes. The keepers are controlled by the Citadel. Before each invasion, a signal is sent through the station compelling the keepers to activate the Citadel relay. After decades of feverish study, our scientists discovered a way to alter this signal. Using the Conduit, they gained access to the Citadel and made modifications."

Shepard's face lit up. "And now Sovereign sent his signal, the keepers ignored him and that's why he needs Saren on the Citadel to control the systems manually."

Vigil's interface seemed to twitch. "The one you call Saren will use the Conduit to bypass the Citadel's defenses. Once inside, he will transfer control of the station to Sovereign. Sovereign will override the Citadel's systems and manually open the relay. And the cycle of extinction will begin again."

"We have to stop him, now," Shepard said, turning to leave.

"Take a copy of this data file with you." The interface on a terminal blinked urgently. "When you reach the Citadel's master control unit, upload it to the station. It will corrupt the Citadel's security protocols and give you temporary control over the station. It might give you a chance against Sovereign."

"It might?"

"We could never test it. When our team went through the Conduit, it was already too late. We could only give the next civilisation a chance to fight the Reapers."

Liara stepped forward, worry on her face. "What happened to the team that went through the Conduit?"

"The Conduit is only a prototype. The portal only links in one direction, so they were trapped on the station. I do not know what became of them then. It is unlikely they found any food or water on the station. I fear they suffered a slow, grim death. I only know they succeeded in their mission to seal the relay. Your presence here proves their sacrifice was not in vain."

"How did this project stay hidden?" Liara asked, gesturing at the massive structures around them.

"All official records of our project were destroyed in the initial attack on the Citadel. While the Protheas empire came crashing down, Ilos was spared. We severed all communication with the outside and our facility went dark. The personnel retreated underground into these archives. To conserve resources, everyone was put into cryogenic stasis. I was programmed to monitor the facility and wake the staff when the danger had passed."

"We scanned the cryopods," Tali said. "They are all dead." Vigil's light dimmed. "The genocide of an entire species is a long, slow process. Years passed. Decades, centuries. The Reaper persisted. And my energy reserves were dwindling. I began to disable life support of non-essential personnel. First support staff, then security. One by one their pods were shut down to conserve energy. Eventually, only the stasis pods of the top scientists remained active. Even these were in danger of failing when the Reapers finally retreated back through the Citadel relay."

"So many people, killed while in stasis," Liara whispered.

"This outcome was not completely unforeseen," Vigil continued. "My actions were a result of contingency programming entered on my creation." Wrex grunted. "I bet they didn't tell the 'non-essentials' staff about this contingency." "I saved key personnel. When the Reapers retreated, the top researchers were still alive. My actions are the only reason any hope remains. When the researchers woke, they realized the Prothean species was doomed. There were only a dozen individuals left, far too few to sustain a viable population. Yet they vowed to find some way to stop the Reaper from returning. A way to break the cycle forever. And they knew the keepers were the key."

"What about the beacon on Eden Prime? And the one on Virmire? Did they program them?" Shepard asked, massaging her temple.

"At our apex, the beacons spanned the breadth of our empire. We used them as a single galaxy-wide network, to transmit data and communications rapidly from world to world. Virtually all the beacons were destroyed during the invasion. But once the Reapers were gone, the survivors here on Ilos decided to risk sending out a message. We knew it was unlikely there were survivors. But if there were, we wanted them to know about Ilos. We wanted to give them hope. So a message was sent across the network."

"Risky," Garrus said. "You could have exposed yourself to the Reapers." Vigil's light dimmed further. "In truth, we didn't expect any of the beacons would still function, but we had to try. If there were survivors, we had to reach them. The message was meant for our own people. It was coded so only organic beings could interpret it. We still didn't understand the power of Reaper indoctrination. We never realized it could lead an agent of the machines — like Saren — to this world. But it has also led you here. So perhaps we did not fail after all."

The VI interface was almost dark now and it was flickering more rapidly.

"My energy reserves are almost depleted. I've dropped the shield in front of your vehicle but I won't be able to stop the one you call Saren much longer. But he has not reached the Conduit. Not yet. There is still hope if you hurry."

"Thank you," Shepard said, waving her omni-tool over the prothean terminal. "I got the file, let's go."

She ran back towards the elevator. Looking over her shoulder, she called back, "Liara, come on!"

Liara was still standing at the dimmed interface, wringing her hands. "I have so many questions."

Vigil's voice seemed to become weaker. "You are asari. My people had high hopes for your kind."

"You knew us?"

The interface went dark. Vigil's voice came from the walls of the caverns, tinny but encompassing. "You must go now. Stop the cycle. This galaxy needs hope"

"Liara, now!" Shepard ordered. The cadence of her voice of made Liara snap to attention and she ran back to them, crashing into Wrex inside the elevator.

"I'm sorry."

Wrex grunted and peeled Liara off him. "And they say asari are so squishy."

"I wish we could have stayed longer, asked more questions," Liara said wistfully. "What their world was like, how they lived before the Reapers attacked."

"Probably hit each other over the head like everyone else," Wrex rumbled. "And enslaved lesser creatures along the way."

"How can you say that?" Liara looked like Wrex had personally insulted her.

"Become old like me," Wrex said, "and you'll see."

Liara glared at him but held back. The elevator opened on the upper floor and they hurried back into the Mako. Madhav drove the Mako forward as soon as the door had closed.

Garrus sat down next to Shepard, took off his helmet and looked at her. She was pale and unusually quiet. "Hey," he said quietly.

She gave him a small smile. "Hey."

"What's the matter, Sunshine?" He had a feeling he already knew why she was so quiet but he wanted to hear it from her.

"It's so much bigger than we thought. A cycle that has been repeating over and over again, indoctrination, more Reapers. Nobody is going to believe that, no matter what I say."

"I took a recording," Garrus said and checked his omni-tool. The distortion made it difficult to understand but at least they had something. They could improve the recording later.

"Oh, good thinking. As soon as we're in Citadel space, upload that somewhere public."

"You think the Council would hide this?"

"I'd bet my pistol on it," Shepard said with an angry frown. "They don't want to hear this, mark my words."

The tunnel was winding further down, passing endless rows of cryopods overgrown with vegetation. A few geth attacked them, but nothing they couldn't handle with their combined firepower and the Mako's cannons.

They rounded a corner as they shot at a geth armature and saw that the tunnel ended. Right at the end, a miniature mass relay was glowing, its rings spinning.

"This must be it," Tali said. "I had no idea a relay could be made in this size."

"Now what do we do?" Garrus wondered.

"We take the Mako through it," Shepard said and gestured to Madhav to let her take over the controls.

"The Mako?" came from many voices.

"I'm so not walking through a mass relay dislocation," Shepard said. "And I don't see the TAP here, so Saren must have taken it through that relay."

Garrus took out two geth troopers that got a bit too close and closed the hatch. "Strap in," he ordered. Around him, seat belts fastened with clicks just like his own.

"Ready?" Shepard asked, her fingers tightening over the control sticks.

"Ready, Commander."

The Mako's engine roared and then Shepard careened towards the miniature relay at full speed, ignoring the remaining geth shooting on either side. The spinning wheels filled the Mako's front screen, the light blinding bright. The familiar gravitational pull grabbed the vehicle, pulling it along just like a spaceship. The noise of the relay stopped and darkness enclosed them.