(Following the Escape from Earth, before the Normandy can travel to the Citadel to gain the help of the Council, as Anderson told Shepard to do, an emergency call comes in from Admiral Hackett – the call is heavily garbled)

Hackett: Shepard... sustained heavy losses...force was overwhelming... There's no way we can defeat them conventionally..."

Shepard: Anderson's already ordered me to the Citadel, to talk to the Council.

Hackett: First, I need you... iance outpost on Mars... ore we lose control of the system...

Shepard: Yes sir.

Hackett: ….been researching the Prothean Archives with Dr. T'Soni...found a way to stop the Reapers... only way to stop them...in contact soon. Hackett out."

Shepard: Joker. Set a course for the Mars Archives.

(Shepard and company arrive at the Mars Archives and encounter Liara after she headshots a pair of Cerberus troops after freezing them in a biotic field)

Liara: But... why'd you come here?

Shepard: Hackett ordered us to come. Said you'd know what was going on.

Liara: I do. (pause) Maybe. I've discovered plans for a Prothean device. One that could wipe out the Reapers.

Shepard: Here? On Mars?

Liara: In the Prothean Archives, yes.

Shepard (WE'RE JUST LEARNING THIS NOW?): We've known about the Archives for decades. Why now?

Liara: Process of elimination, mixed with a little desperation.

Liara: Hackett knew it, too. He contacted me, asking if I would use my resources as the Shadow Broker to find a way to stop the Reapers. My search led me here. Hackett got me access to the Archives and kept me updated on your status. I meant to come see you, but...

….

Liara: In any case, my work paid off. The Archives are full of data. An overwhelming amount. I think I found what we need.

Shepard (SEEMS TOO GOOD TO BE TRUE): I guess I'll believe it when I see it. Where do we find this weapon?

Liara: It's not a weapon... not yet. It's plans for a device. A blueprint.

Shepard (Shrugging): It's more than we had a minute ago. How do we get in?

Liara (Pointing out the window): The Archives are just across that tramway....Assuming Cerberus hasn't locked it down.

Shepard: What are they after?

James: Yeah, they seem hell bent on catching you.

Liara: They want what I'm here for... what we're all here for.

Shepard: But why?

Liara: The Protheans came close to defeating the Reapers. They had plans to destroy them, but ran out of time.

Kaidan/Ashley: And anything powerful enough to destroy the Reapers...

Shepard: Just might be something Cerberus would be interested in.

….

(Liara views the footage of “Doctor Eva Core” eliminating the security crew and venting the Archives upper levels to Mars atmosphere)

Liara: I should've realized it when I met her. I was just so focused on finding a way to stop the Reapers.

Shepard (DON'T BLAME YOURSELF): Stopping the Reapers is the only thing we should be focused on. It's not your fault.

Liara: But what if we're wrong? What if there's no way to stop them? What if these are our last days and we spend them scurrying around trying to solve a problem we can't fix?

Shepard: Liara...

Liara: I know. I shouldn't think that way. I don't know how you do it. You've always stayed focused, even in the worst situations.

Shepard (I REMEMBER THE ONES I LOVE): When there's so much at stake, I think about my friends, loved ones... what I'd lose if I failed.

Liara: Me too.

Shepard (rubs Liara's face): We'll stop them, Liara. Together.

Liara: I believe you. Or I believe that you believe. Maybe that's enough.

…

(Shepard and company enter the core data vault of the Mars Archives after fighting through a million Cerberus troopers.)

(A nearby hologram turns into the Illusive Man)

Illusive Man: Shepard.

Liara (turns and points pistol at the hologram): Illusive Man?

Illusive Man: Fascinating race, the Protheans. They left all this for us to discover, but we've squandered it. The Alliance has known about the Archives for more than thirty years, and what have they done with it?

Shepard: What do you want?

(Hologram of the Illusive Man stares at the Prothean Data Vault at the center of the Mars Archives)

Illusive Man: What I've always wanted. The data in these artifacts holds the key to solving the Reaper threat.

Shepard: I've seen your solution – your people are transformed into monsters.

Illusive Man: Hardly. They're being improved.

Shepard: Improved?

Illusive Man: That's what separates us, Shepard: where you see a means to destroy, I see a way to control – to dominate and harness the Reapers' power. Imagine how strong humanity would be if we controlled them.

Shepard (YOU'RE WASTING TIME): Earth is under siege, and you're hatching a scheme to control the Reapers?

Illusive Man: You've always been shortsighted. Hasty. Your destruction of the Collector base proved that.

Shepard: That base was an abomination. Hundreds of thousands of humans were murdered there.

Illusive Man: This isn't your fight any longer, Shepard. You can't defeat the Reapers, even with the Prothean data.

Shepard (HELP ME, THEN): Work with me. Give me control of your resources, and I'll stop them.

Illusive Man: You'd do better than most, but the odds aren't in your favor. More importantly, I don't want the Reapers destroyed. We can dominate them, use their power, harness their very essence to bring humanity to the apex of evolution.

Shepard (YOU'RE DELUDED): You've gone too far. The Reapers will kill us all if we don't stop fighting each other!

Illusive Man: I don't expect you to understand, Shepard. And I'm certainly not looking for your approval. You were a tool, an agent with a singular purpose. And despite our differences, you were relatively successful. But like the rest of the relics in this place, your time is over.

Shepard: Enough talk. Liara.

(Liara walks to a console)

Illusive Man: Don't interfere with my plans, Shepard. I won't warn you again.

Shepard: Duly noted.

Liara: Shepard!

Shepard: What?

Liara: The data. It's not here.

(Illusive Man Hologram turns away and disappears)

Liara: It's being erased.

Illusive Man (in his office): Goodbye, Shepard.

Shepard: Damn it. How's he doing it?

Liara: It's local. Someone's uploading the information.

(The Virmire survivor walks around and notices Dr. Eva Core at a console)

Ashley/Kaidan: Hey! Step away from the console...Now!

(Eva attacks the Virmire Survivor and drives an omni tool into a control panel, causing the lights on the Prothean Data Vault to dim before running away)

Ashley/Kaidan: She's got the data!

– – – – – – – – – – – – – – – – – – – – – – – – –

(The Normandy is enroute to the Citadel now with the Virmire Survivor in the medbay. Shepard has a QEC conversation with Hackett)

Hackett: Did you get the data?

Shepard: Most of it. He downloaded some before I could stop him. EDI and Liara are analyzing what we recovered.

(Liara enters the QEC room)

Hackett: What have you learned? Was it worth the effort?

Liara: Preliminary evidence suggests the data is a blueprint for a Prothean device.

Hackett: Device?

(Liara plays with her Omnitool and a 3D hologram of a large device appears next to Hackett)

Liara: A weapon, massive in size and scope, that's capable of unquantifiable levels of destruction.

Hackett: Send me the data. We'll do our own analysis. If Liara's instincts are right, this might be the key to stopping the Reapers.

– – – – – – – – – – – – – – – – – – – – – – – – –

(after Hackett's conversation ends, Liara and Shepard leave the QEC room and converse in the Normandy's new War Room)

Liara: I've looked at the data. This weapon could be the answer... if we can build it. I get the sense you don't quite believe it, though.

Shepard: You didn't see what they did to Earth. How is one weapon supposed to stop them?

Liara: What are our options? You know we can't win this conventionally.

– – – – – – – – – – – – – – – – – – – – – – – – –

The First Council Discussion
(after escaping from Sol and arriving at the Citadel)

– – – – – – – – – – – – – – – – – – – – – – – – –

Shepard meets with Liara in her new office on the Normandy after the Council Meeting

Shepard: So you have access to your resources?

Liara: What I can get. We'll need it to research this Prothean device. Until we understand precisely what it does, it's far too dangerous to use.

Shepard (DID THE PROTHEANS FINISH IT?) Did the Protheans actually complete this weapon?

Liara: You mean, “Will it work?” They wouldn't have poured their last resources into the Crucible if they thought otherwise. But we really need to find out just what kind of weapon they left us.

Shepard (AGREED): It'd be nice to know we're not kids playing around with a loaded gun.

Liara: Absolutely. The damage it could cause if it backfired is unthinkable.

– – – – – – – – – – – – – – – – – – – – – – – – –

Shepard talks with Hackett after recruiting Garrus on Palavern's moon

Shepard: Has your analysis of the Prothean device turned up anything?

Hackett: Liara appears to be right. It's a weapon of some sort. A big one. Beyond that, we really can't say--other than it's going to be a hell of a thing to try and build.

Shepard: Do you think it's risky, building something like this when we don't even know what it does?

Hackett: To be honest, the thing scares the hell out of me, but the Reapers have forced our hand. Two centuries ago, scientists faced the same problem in the Second World War. They weren't sure what the atomic bomb might do. Some thought it could even ignite Earth's atmosphere, but they did it anyway.

– – – – – – – – – – – – – – – – – – – – – – – – –

Javik meets the Prothean AI in the Temple of Athame

(a green glowing ball comes from the shattered statue of Athame, revealed to be a Prothean Beacon. It comes to a stop in front of Shepard, Liara and Javik.)

Prothean VI: Obtaining chronological marker. Hold...Timescale established. Post-Prothean cycle confirmed.

Javik: One of our computers.

(VI suddenly rises up and scans the skyline of Thessia, with Reapers in the background)

Prothean VI: Reaper presence detected. This galactic cycle has already reached its extinction terminus.

(VI lowers back to ground level)

Prothean VI: Systems shutting down.

Liara: Hold on!

Shepard: We need answers!

Prothean VI: To what question?

Shepard: The Catalyst. We need to know what it is to finish the Crucible.

(Glowing ball of light transforms into a shaky Prothean hologram)

Javik: A memory... of one of my people.

Liara (If Javik has not been found): “Is that...a Prothean?”

Prothean VI: I am called Vendetta, an advanced virtual construct of Pashek Vran, overseer of the project you refer to as “Crucible.” He died fighting the Reapers in the battle of Tranbir Nine. Your remaining time is also at an end.

Liara: Were all Protheans so grim?

Shepard (THE CRUCIBLE): What happened to the Crucible in your time? Why didn't the Protheans deploy it?

Prothean VI: We were sabotaged from within. A splinter group argued we should dominate the Reapers rather than destroy them. It fractured our order of battle. Later, we discovered the separatists were indoctrinated.

Javik: I always suspected as much.

Shepard: And now we're facing the same problem.

(Hologram changes to show a galaxy map)

Prothean VI: Our studies of past ages led us to believe that time is cyclical. Many patterns repeat.

Shepard: Like the Reaper attacks.

Prothean VI: And beyond. The same peaks of evolution, the same valleys of dissolution...The same conflicts are expressed in every cycle, but in a different manner. The repetition is too prevalent to be merely chance.

Liara: We assumed the Reapers were responsible for the pattern.

(Hologram reforms into Prothean form)

Prothean VI: Perhaps. Though I believe the Reapers are only servants of the pattern. They are not its master.

Shepard: So who is the master?

Prothean VI: Unknown. Its presence is inferred rather than observed. The only certainty is its intention...Galactic annihilation. You now stand at that precipice.

(hologram reforms into an image of the Crucible)

Prothean VI: The Crucible is not of Prothean design. It is the work of countless galactic cycles stretching back millions of years. Each cycle adds to it. Each improves upon on it. Thus far, none have successfully defeated the Reapers with it.

Shepard (GIVE US A CHANCE): Then we'll be the first. Tell us what the Catalyst is.

Javik: Listen to the human. He/She can be trusted.

(Hologram approaches Javik)

Prothean VI: I detect you are one of us. You are Prothean.

Javik: The last. I am the final hope to avenge our people.

Prothean VI: Your mission was known to me. Do you believe this present cycle can deliver retribution?

Javik: They have earned the right to try.

Shepard: Tell us what we need to know

Prothean VI: Very well. If you have followed the plans for the Crucible, I will interface with your systems and assist with the Catalyst to –

(it pauses and shifts into ball form)

Prothean VI: Indoctrinated presence detected. Activating security protocol.

(Kai Leng approaches)

– – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – – –

Conversation with the Prothean VI on Cerberus HQ

https://www.youtube.com/watch?v=fK1D0UnzzRA

(EDI activates the AI from a panel in the Illusive Man's office)

Prothean VI: Online. Security breach detected.

Illusive Man: Enjoy your little chat, but don't overstay your welcome.

(Illusive Man's hologram winks out)

Prothean VI: You are attempting to recover me from indoctrinated forces?

Shepard: Yes. I need to know what the Catalyst is!

Prothean VI: Security protocols have been overridden. I will comply. The Catalyst enhances dark energy transmissions and coordinates the entire mass relay network. In your cycle, it is known as the Citadel.

Shepard: What?

Prothean VI: The Catalyst is the Citadel.

Shepard: So the Crucible and Citadel together, can stop the Reapers?

Prothean VI: That is correct.

Shepard: But... the Citadel was built by the Reapers.

Prothean VI: The plans for the Crucible were passed down to us from the previous cycle, and countless cycles before that. At some point--it is difficult to pinpoint when – the Crucible plans were adapted to incorporate the use of the Catalyst. Presumably, the Crucible was not sufficiently powerful to defeat the Reapers.

EDI: So we use their own technology against them.

Prothean VI: Precisely.

Shepard (WHY ALL THE SECRECY): Why couldn't you tell me this before?

Prothean VI: It was feared that if the Reapers were aware of the Catalyst's intended use, they would retake control of it. I am programmed to withhold that information until the Crucible is complete.

Shepard: It's as ready as it's going to be. Let's get it to the Citadel.

Prothean VI: That may no longer be possible.

Shepard: Why not?

Prothean VI: The one who broke through my security protocols, the one you call the Illusive Man, has fled to the Citadel and informed the Reapers of our purposes.

Shepard: Damn it!

EDI: Then the Citadel is in danger. The Reapers will take control of it.

Prothean VI: They already have. The Citadel has been moved to the Reaper-controlled space.

Shepard: Moved? To where?

Prothean VI: To the system you refer to as Sol.

Shepard: Earth.

Prothean VI: Correct. The Reaper forces will now consolidate power around the Catalyst and protect it all costs. The odds of accessing it are remote.

Shepard (WE'LL BEAT THE ODDS): Don't count us out yet. We've come this far, and we'll finish this. We'll get the Crucible to Earth.

Prothean VI: I hope you find success.

Shepard: EDI, get me Hackett. He needs –

(Kai Leng enters and a fight scene ensues in which he's defeated. While Shepard moves to look at the Illusive Man's computers, Kai Leng slowly gets up and starts walking towards Shepard and tries to stab them in the back, but RENEGADE INTERRUPT kills him)

Shepard: That was for [$NAME$], you son of a bitch.

(as Kai Leng falls down, the Prothean VI reappears)

Prothean VI: The Citadel is in position. The Reapers are preparing to complete their harvest of your species.

Shepard: I'll stop them.

Prothean VI: It is too late. I recommend investigating a means of conserving information for future species.

(Rengade Interrupt option)

Prothean VI: Perhaps you will succeed where we failed. Perhaps your warnings will be heard early enough.

(Paragon interrupt option)

Shepard: You didn't fail. You gave us a chance. And we're not done yet.