After stopping Ironwood, Razer and Aya along with Saint Walker and the rest of Ruby's group began making their way to the Atlas Vault. On the way there, Penny's condition worsened.
Ruby: As soon as Penny opens the door, we go through, grab the Staff, and stop her termination.
Razer: We'll get Penny the help she needs. I promise.
Penny's condition worsened to the point where she could barely walk. Aya and Ruby carried Penny to the entrance to the Vault. When they reached the entrance to the Vault, Penny used her Maiden Powers to open the door. As they enter the Vault, they found themselves on a stone platform with the Staff of Creation. As Ruby grabbed the Staff, a muscular, blue-skinned figure takes form before them and flexes gratefully. Upon seeing this, everyone was taken aback.
Saint Walker: I have seen many things in my life, but nothing quite like this.
Ruby: Ambrosius.....
Ambrosius: Ah! It seems someone has come to engage my creative wiles! All I'll say is it had better be worth it after my last project.
Ruby: Hi, um, Mr. Ambrosius? Sir, listen, it's about our friend. She's... She's dying.
Ambrosius: I'm going to go ahead and assume that you know it's against the rules for me to bring people back from dead so...
Ruby: That's not what we want. She's not your typical girl.
As Ruby says this, Ambrosius becomes interested. Upon examining Penny, he quickly realizes that she is in fact an android with a soul.
Ambrosius: So she isn't! I'd love to meet whoever did this. Ah, I see. There's something eating away at her. I'm guessing you think you have some clever plan to save her. Just know, I will give you exactly what you ask for and I don't want any complaining when it's not what you wanted.
Ruby: We brought her schematics. We want you to make a new version of her using her exact same robot parts.
Ambrosius: That was curiously worded, girl.
Ruby: An exact copy of her would include the virus. An exact copy of her without the virus would cease to exist the second you make something else, and we kinda wanna keep her around longer than that.
Ambrosius: You've done your homework.
Aya: Anything for Penny.
Ruby: We want you to create a new version of her, using her existing robotic parts taking the virus with them.
He makes an expansive gesture, then makes some more hand movements, a bright glow emanating from his hands. A stream of sparks and mist moves toward Penny and snakes around her, lifting her into the air. As time resumes for her, she blinks and the red glow of the virus disappears from her eyes. She glows brightly, causing Razer, Aya, Saint Walker and Team RWBY to shield their eyes. Her extremities shimmer, and when Ambrosius gives a final snap of his fingers, two identical Pennys stand beyond the vault's threshold.
Ambrosius: It's done!
As the process was finished, they saw the two Pennys clearly. Once was the remains of a robot while the other was a living human girl. Everyone was shocked by this. Without hesitation, Penny hugs Ruby. The sensation she felt was unlike anything she's felt before.
Aya: Penny. How do you feel?
Penny: I.....I feel wonderful!
Aya glanced over to see the robotic remains of Penny's original body. It seemed strange to Aya that her sister was now human. Despite this, Aya was happy with Penny.
Weiss: We should probably make sure our theory works. And start the evacuation.
Razer: We're low on time. We need to find a way to evacuate the people of both Mantle and Atlas evacuated quickly and safely.
Ambrosius: Sure! I'll just need coordinates and specs for each door, an explanation for bending space and time to account for the much greater traffic on one side and the single point of exit on the other.
Weiss: Okay, that's about what we expected. So, we need to funnel everybody through a central location first.
Ambrosius: You're going to have to tell me more about this central location. For starters, uh, where is it?
Yang: Here. A place like these Vaults. Wherever they are, they're not part of Remnant. Only accessible if you know the right way in. Seems like a safe enough place for thousands of refugees.
With the logistics explained and maps presented to him, Ambrosius makes it so. He creates a doorway that creates multiple portals leading them into an extradimensional space that leads them to Vacuo.
Weiss: People enter from Atlas and Mantle on one side... and leave on the other side, with a one-way ticket to Vacuo.
Ambrosius: Well, everything appears to be in order. You were quite thorough, disappointingly so.
Weiss: So it's done?
Ambrosius: Yeah.
Saint Walker: Thank you for your help. We are in your debt.
Ambrosius: Oh, and one last point of clarification about this central location of yours. Do not fall.
With that, the group took this warning to heart. As Ambrosius vanished, Weiss takes hold of the Staff.
Weiss: We did it!
Penny: What now?
Ruby: We go to Vacuo, all of us, and hope that we've thought of everything.
Blake: Finally. Things are going right for us. If we can get the people of Mantle and Atlas to Vacuo, then we we're finally one step ahead of Salem.
As Ruby's group moved, Razer was troubled.
Aya: What's wrong?
Razer: All of this has gone well. Too well.
Aya: You speak of the Red Lanterns.
Razer: Yes. I've seen Red Lantern invasions time and time again. Should we succeed in evacuating the people of both Atlas and Mantle to Vacuo, will we find Red Lanterns waiting for us?
Saint Walker : I don't know, but we'll figure something out. We always do.
With that, Razer and Aya along with Saint Walker moved to help with the evacuation. In that moment, the group finally had the means to save the people of both Mantle and Atlas from the wrath of Salem. But what they didn't know was that dark forces were in play as the forces of Salem closed in on both Atlas and Mantle, ready to strike the final blow that would bring about the destruction of the two cities.