(I imagined this scene when debating with myself the direction RWBY would be heading in future seasons. I argued that, since Ruby has a kind of "simple soul," comprised of hope and friendship and the desire to help people, part of the future for the series would be testing that soul, the very essence of Ruby's character, in harsh ways. This was an idea that stuck with me.)
Ruby tightened her grip on Crescent Rose, seeing the path before chained by Aura thread roared and raged at her appearance, their paws pounding at the bars of cages set in alcoves that were carved along the hallway. The immediate sound was not only annoying but slightly jarring as well, and itput a damper in her plan. Ruby sighed.
"Quiet!" Yang punched a solid portion of wall. The luminescent shockwave ran along the hallway, loosening and setting the cell bars in ringing vibration. The Grimm replaced anger with whimpering and retreated into the backs of their homes. Not silence exactly but a much better reaction.
"Think they heard us?" Yang asked as she followed the lead her sister set, chipper as always.
Ruby sighed, watching the cracks in the stone at her feet as she walked. "The Beowolves? smashing the wall? Maybe the faculty'll think it was an earthquake. A short, isolated earthquake."
"Well, you never know. They made Penny, after all, and there was all that equipment we passed by. They could be faking earthquakes. Hey, why do you think they have all these Grimm captured? It's not like they couldn't afford an alarm."
"I don't know, and right now I don't care. I just want to find Penny, make sure she's safe, and get out of here. I hate labs."
They still had a ways to go. The soulless creatures they passed now weren't whimpering, but thankfully they weren't barking either.
Yang caught her sister's downcast expression. "Ruby, what's wrong?"
"I'm worried about her, Yang. I like her."
"You barely see her. You hang out with Ozpin more than you do with Penny."
"I'm with Penny all the time."
"Like when?"
"Whenever you're out with your friends. It's not like we spend all our time with the guys from school." Ruby started to smile, thinking back on the last few years, when they hadn't been in peril or chasing terrorists. The epic food fight, Jaune showing them that dumb comic book, and just last week the five-minute soda drinking contest followed by the hour-long burping contest. Those little moments she thought of when thinking of her friends.
Her smile faded. "Penny's my friend, too, Ruby."
"If she was, you'd be worried about her more. She's been acting up lately and her father's really been keeping her on a tight...leash." They stopped at the last inset cage, which held the hallway's final Beowulf. It was tied against the far wall by at least three Aura strings, the same kind Penny used with her swords. It didn't try to break free and attack, it barely growled, more of a warning than a threat. They had talked their way through it, but Ruby admitted that the hall was foreboding. A man who could build a whole girl, who could conquer the world's greatest threats with just a few strings, was a powerful and driven man. What would they do if he wouldn't give Penny up?
Ruby slipped the keycard Weiss had gotten for her through the reader on the door. A moment passed and the red light shifted to green with a satisfied beep. The heavy steel door opened on its own, with the hiss of pressure releasing. To Yang, and Ruby in particular, the pressure was rising. After the thin hallway they had just cleared, the final room was a surprise. It was large, dome-shaped but made of irregular square panels, and nearly empty, undefined. No ornamentation anywhere, no change in the climbing, encompassing walls except for a glass observation box on the far end. The shadow of a man stood in that box, at a console, holding a microphone to his lips.
"Good evening, Huntresses-in-training. I was not aware Penny had scheduled a playdate."
The sisters stepped further into the room. The door now behind them closed. Except for a cautious over-the-shoulder glance, they paid it no mind.
"Where's Penny, Mr. Polendina?" Ruby demanded. Her voice echoed back to her.
Yang looked to her right. "Whoa, Ruby, don't get edgy just yet, we don't even know—"
"I'm sorry, Penny is dead, you see," the man calmly said.
"What!" The red-haired Huntress dashed forward a few steps, stopped suddenly. "What do you mean? She's only been here! Where is she and what did you do to her?"
The man chuckled, as if he hadn't've just admitted his daughter was gone. "Right, she's been here for her operation. Her body's fine, and the template, but her mind, you see, was getting too unruly. Disobeying me, going out, jeopardizing years of work. Normally I'd be angry—I'm not a patient man, you see—but we found an easy shortcut, so no harm done."
Before Ruby could piece together a response, Penny's father moved slightly to press a button on the console in front of him. Something under the room hissed, Ruby by reflex dipped into an action-ready pose and edged away, one hand on the folded Crescent Rose at her back. Several tiles in the center of the room descended, only to rise again carrying something. An operating table, Penny laid out on it,tilted so that she was nearly standing. She blinked.
"Penny!" Ruby leaped forward as Yang, fearing a trap, called her name unheeded. Ruby embraced her friend. She seemed to be free, but up close she realized the robotic girl was strapped down by more Aura string.
Seeing as how nothing attacked them, Yang took a few steps forward, not towards Penny but to the observation box. "If you think joking about your daughter like that is funny then you need to read a joke book before picking up any more textbooks!"
"I am designated as Penny Polendina Artificial Aura Attempt Zero Zero Two. I have been authorized to accept the title of Penny. Current status: Not combat ready. I require more data."
"What? Penny, what are you saying?" Ruby released her friend. It was her voice, that was unmistakable, but it wasn't her at all. She looked in the robot girl's eyes—they did not see back into hers.
"I was not joking, Yang Xaiolong. I do not joke." Ruby listened, but did not look at the man. She was still staring in confusion at Penny's body. "You were part of the problem, you see. You two and your other unsavory cast of friends corrupted Penny Zero Zero One. Shame, because she came so far, and first attempts rarely do. We extracted the data we needed, analyzed it, and wiped the mind for a fresh slate. Now that she's been formatted and the Gippet-OS reinstalled we can restart, use the good data, and create not only a better Penny but a more manageable one to complete our goals."
"Penny?" Ruby had spoken, Yang looked at her. She seemed in a trance, tears unfallen building in her eyes, like a program looping the same operation, getting the same answer that didn't fit. She was both comprehending and not comprehending at the same time.
She shook her head. "No, she has to be in there. Penny. Penny, if you can hear me, say something."
"I am designated as—"
"No! The real Penny! Let the real Penny talk!" Ruby was on the verge of hysterics, her grip on Penny's striped dress shaking. The body silenced itself. It smiled at Ruby but its eyes were blank.
"You're sick!" Yang screamed at the man behind the glass, so far up. She wanted badly to jump up there and let her fists show how much she felt, but composed herself. Only one of them needed to be unstable at a time, and right then it was Ruby. It was her job to watch over her sister. "Ruby, we need to get out of here. We'll go to the police, tell them that—that Penny's been murdered. We need to—"
"How can you say that?" Ruby snapped at her sister, spinning away from but still gripping the body on the table. "She's not dead. She's right here, her body is right here, she's still in there somewhere."
"Penny was deleted last night, you see," the man said. "She is gone."
Yang took hold of her sister and yanked her away. She hauled Ruby closer to the sealed door, trying to fight against her struggling.
"I'm afraid I can't let you do that, young Huntresses." Yang stopped to listen. "You see, Penny Zero Zero One was a registered citizen, because her mind was very advanced. Our government recognized her as a person, not as the machine and tool she was. If you went to them, I would be arrested. You see, I can't have that."
Ruby kicked and clawed at her sister, trying to break free. "I can save her, I can get her back, Penny's in there! You can't just erase a person."
Yang with one hand started to punch the door. It dented, started to give.
"Penny Zero Zero Two, observe combat abilities."
"Not combat ready. Insufficient data," she piped cheerily, her natural inflection.
"Hmm, pity. Well, at least it was only a few hours lost. Penny Zero Zero Two, voice authorization. Activate short-fuse self-destruct sequence."
Penny didn't hesitate in announcing her death. "Voice authorized. Self-destruct sequence activated. Twenty seconds remaining."
Penny's father was still calm. "Well, girls, it has been fun but I must put in an order for a new body. It shall be so sad reporting that you and my dear Penny lost your lives due to untimely hardware failure." He left the box.
"Penny, no, don't!" Ruby screamed, her sister holding her just by one hand as she worked on the door. The robot counted down the seconds.
"Almost there." Yang muttered to grit teeth. She could see the hallway on the other side through cracks in the steel. Ruby broke away from her grip and dashed towards Penny with her Semblance speed."Ruby, no!" One more hearted punch and the door flew down the hall. The shockwave again rattled the bars of the Beowolves' cages.
Yang turned in the same motion, started to run after her without hope of catching up. "Ruby!"
The red-haired Huntress reached her first, of course. "Penny, stop this, I won't leave you here, I won't fail."
"Voice recognition activated," the robot stated. "Recognized designation Rose comma . Friend—Error: data missing."
It was all Ruby needed. "Penny, Penny, stop the countdown, stop the countdown, don't self-destruct!" She wrapped her arms around Penny's neck, pleading. Yang wrapped her own arms around Ruby's neck—but instead of pleading, ripped her away, tried to force her to their only exit.
"Zero seconds. Self-destruct sequence activated."
Yang screamed, rushing towards freedom. Penny screamed for the briefest moment as the burning light from inside her own body tore her apart. Ruby screamed too, shrieked Penny's name, high and shrill at first, and even more so on the second syllable. The room collapsed around them, metal screaming against metal as it fell.
(In my mind, this was a season finale. This was the last you saw for a while. The light from Penny enveloped the screen and did not fade; credits begin to roll, for the first seconds leaving only the screams and chaos. In the post-credits scene, or at the start of the following season if the writers were mean, Ruby is revealed to be otherwise unharmed physically. She is at a hospital with Yang, getting their small wounds healed...and Ruby is holding Penny's burned, torn bow. Over the next season, she would rebound and find comfort in remembering Penny, dealing with her father, and of course with help from her friends.)