When they awoke, they were confined by familiar holding capsules, the same as in the Citadel. They initially struggled, but of course it was futile. At first all they saw was that they were surrounded by soldiers. But then, something came in the room, from the ceiling, suspended by a metal frame. At first, Gordon thought it was an Advisor. A slug was all it was, with only two metallic arms. But there were none of the traumatic mental blasts that usually characterized their presence. Instead, when it stopped, a pair of Stalkers walked up to it and attended it, then walked away.
A moment later, a voice blared out of speakers on the walls.
A voice very familiar, bristling with arrogance and contempt. The voice of Dr. Wallace Breen.
"Doctor Freeman. Alyx Vance. How good of you to join me."
Alyx's face was a mask of shock. "How? How are you alive? You're dead!"
"Of course it may seem to be that way, my dear, but the Combine have abilities you have scarcely dreamt of. I am right here."
He looked at the guards and said to them, "That will be all."
A couple of the guards looked at each other, but then shrugged and left.
As soon as they were gone, the Breen-slug used its metallic limbs to push a button. The first time it tried, it missed, clearly unused to the limbs. The button released them and they were able to open their restraints and get out.
The Breen-slug said to them, "I need your help."
Alyx and Gordon were shocked, to say the least. Alyx just sputtered, "Our help?! Why the hell would we help you?!"
The Breen slug responded simply, "Because what I want you to do-"
It faltered for a minute, then mustered the strength to continue, "-is to kill me."
Alyx and Gordon shot a glance at each other, and then Alyx replied, "Come again?"
The Breen-slug told them, "I'm a slave to the Combine now. And I... I can admit when I'm shown so forcefully when I'm wrong. You have a real chance of defeating the Combine. All I am, now, is a remnant. No longer... no longer human."
It was clearly upset now. Gordon, in all the years he'd known him, had never heard anything but arrogance in that voice, so it highlighted just how much things had changed.
"Judith is below. The Combine have been forcing me to use her to bring the Borealis into phase so that we can board it. You need to do it. Use it to defeat the Combine. And kill me before they do. Or... before they do worse."
The Breen-slug used a limb to access the controls to open the door. "Either way, you're free to go."
Alyx gave a disgusted sound and said to Gordon, "Come on, Gordon, let's go. This is pathetic."
She walked out of the room while Gordon stayed for a moment. The Breen-slug gave him a look that he could have sworn was pleading.
Shortly afterward they were continuing on. It wasn't long before they encountered more soldiers, so they didn't have time to discuss what had happened. They pushed one level down, where there was a room of cells. Only one was occupied- the one populated by Judith Mossman.
She looked pretty rough. She had bruises on her face and blood on her clothes.
She perked up when she saw them. "Alyx? Gordon? Thank god! Get me out of here!"
Alyx just looked furious. "Why should we? You're working for the Combine! Again! How many times have you betrayed us?!"
Mossman responded, "It's not like that. Everything I did, I did to help your father. The Combine let us work on our technology as long as they could have it too. Eli knew everything. He always knew I was working with them. But if I hadn't, they would have stopped us. We gave the resistance a fighting chance-"
"Enough! I've had enough of your lies! Always manipulating! Dad trusted you, and now... now he's gone."
Mossman put a hand on her chest and whispered, "What?"
She sat down. "Eli's dead?"
Alyx kept at her. "It's your fault! All of it! If you hadn't betrayed him, he'd still be here! We should just leave you to rot!"
Gordon wasn't so sure. From what he'd seen, she'd genuinely been trying to help the resistance recently. And she and Eli had seemed to have a genuine relationship. It seemed harsh to be blaming Mossman for that.
Mossman took a moment to compose herself, and then stood and said to them, "Either way, you need me. I've been trying to force the Borealis into reconciliation with our space-time. I know where the resonance keys are. We need to finish this. The Combine can't be allowed to have that technology."
Alyx turned around and looked at Gordon. "On that we agree."
She sighed heavily and headed for the console opposite the cells. A few moments later, the force field went down and Mossman stepped out. She said to them, "Right, let's go."
The next area appeared to be a scientific lab means to work on bringing the Borealis into phase. There were soldiers guarding it, and Mossman hid behind a corner while Alyx and Gordon took care of them. With the lab clear, Mossman accessed a console. She locked the door and then explained as she worked, "It's actually fascinating what's happened. Aperture used a form of quantum uncertainty for their teleporter, and managed to steer the probabilistic reconciliation to a target. But what they missed, which clearly they didn't test for, was that as the distance increases, so does the energy required to reconcile the uncertainty. Because they didn't have enough power, the ship has ended up kind of drifting between where it was and where it is. It's only because the reconciliation has partially taken place that it's visible to us at all."
She shook her head in amazement as she worked on a console. "The work they did was incredible. Beyond anything- okay, here are the resonance keys. With these, we can temporarily reconcile the field."
She looked at a monitor. "Uh-oh. We have company. A lot of it. We need to activate the resonators. There's one here, and two at other stations. They look clear, at least for the moment. But we need someone to protect this one and keep the Combine from coming after us. I'll activate a force field as well."
Alyx thought quickly. "Gordon, while you protect this one, we'll go for the others. We'll be back soon."
There was a familiar beeping sound- a breaching charge. Mossman amd Alyx rushed out of a door and a force field snapped on behind them.
A couple of moments later, two doors simultaneously exploded. The room was fairly large, so there was plenty of room to maneouvre, but it was still a difficult fight.
Shortly after it ended, Mossman and Alyx came back. Alyx said to Gordon, "Looks like you had some fun."
Mossman told them, "More will be coming. I'm bringing the resonators online."
There was a buzzing sound that increased in pitch until it was inaudible. Then, the ever-present lights in the air began to change. They started to move quicker, and become brighter in some places while gone from others. Soon they were all gone, and Alyx looked out the window at the Borealis. "Look!"
They all watched as it became more solid. "Alright, we should board before it goes out of phase again."
Before they could, however, there was an explosion in the distance. Security monitors showed different parts of the facility, where Combine soldiers were fighting against what was initially an unseen enemy. They were defeated, and resistance fighters came into view.
Mossman told them, "This doesn't change anything. We need to get on board, now!"
They fought through Combine soldiers to get to the Borealis, this time at times assisted by resistance fighters. But the fighting was fierce, and whoever was now directing the Combine forces seemed determined to stop them from reaching the Borealis.