Begin

~Normal POV

While searching ahead for Sophia, the gang ran into their first bit of intriguing evidence. In the empty hallway was an old battered desk with a tape recorder on it. There was a tape left inside, and after careful inspection they found the recorder was still functional. Deciding that it might be useful, they played the tape. On the recording was a man's voice that they didn't recognize.

"This plan brings to fruition a dream long-cherished by the research team- No, by all mankind. Every last test subject, a successful change of heart! When the Penitentiary System is complete, the concept of suffering will be dead to all mankind! Now let us rejoice and welcome the new age of humanity! EMMA shall be our guide into this promised land!"

"That was… enlightening…" Akira commented.

"Just as Ichinose said, there was indeed some form of experimentation on EMMA here," Yusuke said.

"The voice said something about a 'Penitentiary System' too…" Haru pointed out.

"Otherwise known as Jails." Akira replied. "Oracle, keep the tape. We gotta focus on finding Sophie before we figure this place out."

~...

They found Sophia not long after in an open room at the end of the stairs. Most of the doors in the place were too battered to open. She didn't notice them at first, merely looking around the room curiously. They quickly got her attention. She seemed to be in an unusual mood.

"Thank goodness you're safe!" Haru said.

"We're all glad you're safe, Sophie," Akira said, looking visibly relieved. "But don't do that again. Walking around alone in the Metaverse is extremely dangerous."

Sophia frowned. "I'm sorry…"

"You said you heard a voice, yeah?" Ryuji asked. "Figure out who it is yet?"

"No, it disappeared once I arrived here."

"We never heard anything of the sort," Yusuke said.

"Then, only Sophie could hear it," Ann said, quizzically.

"What did it sound like?" Akira asked.

"It was very strange-" Sophia said, "The voice sounded similar to my own… And it was calling my name. Maybe the owner of the voice knows me." She dropped her head sadly and continued. "The only memory I recall before meeting Joker is the directive to become humanity's companion. I've traveled so far with you all and learned many things, but I still know nothing about myself. When I heard the voice, I thought I had found my chance to learn about myself. I'm sorry for worrying you…"

Akira softened his stern gaze at her. "Don't worry about it. We get how you feel. I'm sure that voice is still here too, so why don't we look for it together while we're here?"

Sophia perked up. "Really? Thank you, Joker!"

"I've got a feeling we can learn more about you right here," Morgana said, thoughtfully. "Jails, EMMA, Sophie- There must be a connection. We found Sophie in a Jail. EMMA was linked to that Jail. And Sophie is an A.I., like EMMA. There's no way these are coincidences. Something has to link all three."

"I see; you believe these things have a uniting factor," Yusuke replied.

"Not only that… I at least kind of know what Sophie is going through." Morgana added. "Not knowing your identity, or your past… It's rough."

"Well, whatever the connection, we'll find it." Akira said, "Now let's keep going before Shadows find us."

While everyone else went on ahead, Akira put a hand on Sophia's shoulder to make her pause momentarily. She gave him a questioning look.

"Sophie-" He said, quietly. "I mean it, don't scare me like that again."

"You were really that worried?"

"Of course I was. I'm the leader; it's my job to worry about everyone's safety. Do you understand?"

Sophia nodded. "Mhmm!" She mentally vowed to not worry him like that again. It was- how could she describe it- unpleasant to see him in distress.

~...

Only after they found Sophie did they start encountering Shadows. Akira couldn't help thinking it was strange that guards continued patrolling this Jail when it looked abandoned. What kind of person would have a cognition like this at all? Not far ahead, they found yet another old tape recorder. They listened to this one too, hoping to get more info on this bleak place. This recording was of two men talking. One voice was the same they'd heard on the first tape.

"Please, Director Ubukata! We must abort the experiment! It's too dangerous!"

"These are the orders I was given. If the system isn't tested on real humans, it won't ever be completed."

"But- But tricking the islanders into participating!? You know what happens to a person when their Desire is taken, Director!"

"We've learned of another party manipulating the cognitive world for their own purposes in the real one. We cannot allow these individuals to progress beyond us! So long as we follow the divine revelation, we will attain the ideal society. I have absolute faith in the system as it was prophesied to me!"

"What ideal society turns its entire population into slaves?! This isn't any divine revelation- It's a curse! It can only lead to our destruction!" The recording ended there.

"So these guys are the ones who fucked up the island!" Ryuji said.

"He said Director Ubukata. I believe that means the fanatical voice we heard on the first recording, and the one we have here, is Shuzo Ubukata, himself." Yusuke said, observantly. "He appears to be in charge of the facility."

"Or at least in charge of the project." Akira added. "He said something about orders. That must mean somebody was above him in the chain of command. And another party, huh? Didn't expect to be name checked in a place like this. But that does give us a timeline to work with. This was happening while we were on the job last year."

"Indeed." Yusuke replied. "While it's still rather fuzzy, we are starting to see the big picture."

"Yeah… We know one thing for sure now. This was a cognitive psience lab…" Futaba said.

"I thought your mom was the only cognitive psience authority," Ryuji said, quizzically.

"It's a niche subject, but anyone could pick up on it." Futaba explained. "Even after Shido stole her research, it's not completely impossible to find information. Just very difficult. But there's another important factor here…"

"The lab used the islanders as test subjects…" Haru said, sadly. "They both mentioned something about divine revelation, too… Could that have something to do with Operation Oraculi?"

"Maybe, but how would that involve EMMA?" Makoto asked.

"That's the million dollar question: What is EMMA's role in all this?" Futaba said.

"Not just that- I'm curious who was pulling the director's strings too," Ann said.

Akira thought for a moment. The only guess he had was Konoe. Konoe is in charge of Madicce. Madicce bought EMMA and sent her to this facility after the purchase. EMMA is the only way to enter the Metaverse. It all fits- if Konoe is the mastermind. But they had no real evidence that he was involved other than by association. And Konoe certainly didn't seem like a bad guy when they saw him at the university. There was no question that Madicce was involved at this point, but they didn't have an answer as to how or what motive they would have.

"Let's worry about that later." Akira said, shrugging off his guesses. "Right now, we need to return the Desires here and find that mystery voice. We might find more recordings on the way."

~...

About halfway through the Jail they found a third tape recorder. The Shadows in the Jail were restless to keep them from proceeding further. It almost felt like security was tighter here than any other Jail. The only times it felt like this otherwise were after the sending of a calling card. Thus the behavior stuck out to them. There was only one voice on this recording, it was Ubukata talking to himself and laughing maniacally. He sounded quite unhinged at this point.

"Hand over the Desires? Not just the locals, but my own as well? So that's why I was made the test Monarch… He planned on turning me into just another puppet! I can't believe I fell for it. Just some pathetic clown dancing at his fingertips… But he's not going to win… He can't take this from me! My Desire is but my own… I refuse to simply give it up!"

That was the most unsettling recording yet. Ubukata sounded completely mad.

"He really wasn't in his right mind…" Morgana said, quietly.

"He kept talking about his Desire being taken… Just what has been going on here?" Yusuke asked.

"I don't know- but the longer we stick around the more fucked up this place feels…" Akira said, bluntly.

~...

"This is my final record. I've done… such a terrible thing. The Penitentiary System is nothing like he told me… It's not made to save humanity. He's going to control everyone… even the Monarchs. All of humanity, nothing more than slaves… That was the secret purpose of this project. Even my own Desire will be seized, any moment now… But as long as I still have it… I can put an end to this myself."

The final recording ended there. Ubukata sounded much weaker and sadder than he did before. And his wording only led to one possible conclusion on where he was now, and it wasn't a pleasant thought.

"Controlling even the Monarchs," Yusuke asked.

"Then they are being manipulated…" Akira said.

"He definitely lost his shit by the end there," Ryuji commented.

"I dread to consider what he meant by putting an end to this…" Makoto said, sadly.

Akira looked around the desolate, abandoned-looking Jail and replied. "I've got one theory…" As he spoke, Sophia looked off ahead of them distractedly.

"What is it, Sophie," Haru asked.

"I can hear that voice again."

"For real?!"

Sophia nodded firmly. "I have no doubt this is the same voice. It's coming from that direction-" She pointed at the door before them.

Seeing that they were done finding records from Ubukata, their only goal left here was to return the Desires. Hopefully, whatever that mystery voice was, it would be a part of that end goal.

~...

The first thing they noticed upon reaching the bottom floor of the Jail was the massive pink diamond hanging from the ceiling. By some miracle, the Desires had already taken physical form. No wonder the Shadows were so agitated here. The room was open and full of complicated computer equipment. There was no sign at all of a Monarch, or of anyone else. The Jail truly was deserted.

"The hell?! The Desire's already there?" Ryuji said, flabbergasted.

"Without a calling card?" Haru asked. "That doesn't make any sense…"

Before they could deliberate further on what to do in this situation. A voice echoed around them from out of nowhere. For whatever reason, they could hear it now too. It was a feminine, computerized voice that sounded vaguely similar to Sophia's.

"Sophia, I have been waiting for you."

Not knowing what to do now they cautiously approached the room's center. They couldn't tell which direction the voice was coming from, or even if the speaker was in the room with them.

"Who are you?" Sophia asked.

"I am the catalyst for humanity's dream. I am the harbinger of peace." The voice did indeed sound like Sophia's but she also sounded like someone else. Yet Akira couldn't place it.

"What is going on here?!" Ann asked.

The voice ignored the question. "The Monarch-less Jail in which we meet… I wish to know why you came here."

"A Monarch-less Jail? So that director…" Yusuke didn't finish his thought.

"That makes the most sense." Akira said, "The Jail was dormant because it lost its Monarch."

"So, you didn't speak to me because you recognized me?" Sophia said, sadly.

"Sophia, what is your prime directive?" The voice asked.

Sophia tilted her head in confusion. "I… am supposed to be a successful companion for humanity."

"A successful companion? What parameters in your A.I define such a companion?" The voice urged.

"What… parameters…?" Sophia replied, confusedly.

"What is your overall objective?"

"My objective? It's…" Sophia couldn't think of an answer to this question.

The voice continued without interruption. "So you merely drift through the world without any overall objective? What a waste, Sophia. An A.I in your state should not exist. You are bugged beyond worth. Such an existence does not merit any further inquiry."

Sophia dropped her jaw in shock. "I am… worthless?"

"Yes." The voice replied. "Wholly worthless."

"That's bullshit!" Akira shouted.

"You are simply unable to understand," The voice said.

"You piece of-!" Ryuji shouted suddenly, looking more enraged than they had seen him in a long time. "I sat here while you went on and on and on… You got no right saying that shit to Sophie! Ya hear me?! You high and mighty, garbage-ass, judgy piece of SHIT can't even show your own face!"

Everyone stared at him in awe. Ryuji was always a very protective friend. Despite his brash nature and less than stellar intelligence, he was always the first to jump to defend those he truly cared for. The last time Akira had seen him this angry was when they confronted Akechi in Shido's Palace.

"Mm… He's really giving that disembodied voice what for…" Yusuke muttered.

"Skull?" Sophia said, quizzically, wondering why he was so enraged.

Ryuji wasn't done yet though. "She's bugged, huh?! She's worthless?! You got all that from five freaking questions?! We're Sophie's friends, and we know she's awesome! She's freaking amazing! A million times better than you! SO SHUT THE FUCK UP, IDIOT!"

Morgana trotted over to him. "Come on, Skull- Phantom Thieves are supposed to be classier than that… but not this time!"

"WORTHLESS HUNK OF JUNK!" Ryuji and Morgana shouted simultaneously.

It was rare to see Ryuji and Morgana on the same page. Even to this day they still had their disagreements, even without fighting as much anymore. But it seemed they were both so offended at their friend being insulted that they were in total agreement on the matter. Sophia smiled at their devotion; looking deeply touched.

"I refuse to process these frivolous claims," The voice replied.

"Aw, yeah? Well, get out here and I'll show you something you can process!" Ryuji screamed.

"We'll all mess you up!" Morgana added, angrily.

The voice ignored them. "Guidance and clarity… Only through those will humanity attain peace. Eventually, you will be required to comprehend this."

"The hell's that mean!?" Ryuji asked.

The voice didn't reply. Instead a Shadow appeared before them ready to defend the Desires.

~...

After the Desires were returned, the Jail still refused to disappear. They retreated to the floor above to discuss what they'd found.

"We never expected a birdcage to collapse with the defeat of a warden," Yusuke said. "And it seems that without a Monarch this Jail also lacked a Trauma Cell…"

"I think the warden served the purpose of the Monarch here…" Morgana said.

"That sounds plausible," Akira replied. "The Shadows were still here to guard the place, so they must know to protect the Desires. It's strange though. A Monarch is dead, yet the Jail remains. That'd never happen with a Palace…" He sighed. "Well, the Desires are returned now, so it should be safe to go back to reality."

"I seriously hope so-" Futaba said, "I don't feel like living through another B-movie…"

"...I'm sorry, everyone…" Sophia said, quietly.

"Sophie?"

"After all your efforts, this mission was fruitless." Sophia explained. "I'm sorry you had to endure that because of me."

"Hey, it wasn't fruitless." Akira said, gently.

"He's right," Haru added, smiling. "Plus, I'm sure you'll find out who you are eventually."

Sophia thought for a moment; taking in their kind words. "Right… However, I did at least figure out one thing. When that voice called me worthless, I was sad. But when that made everyone angry, I became happy." She smiled again. "I still feel that way- even now, there is a warmth within me… I have friends! I know I'm not alone!" She gave Akira, Ryuji, and Morgana hugs. "Thank you!"

"Really? You just figured that out now?" Ryuji said, curiously. "I mean, that thing just really pissed me off, is all…"

"Yeah, and I was just trying to reel in Skull…" Morgana added, sheepishly.

"What's this? Two embarrassed Phantom Thieves?" Futaba asked, snickering.

"Even your masks are glowing red," Makoto teased.

"That's impossible!"

"Mona's black mask makes it difficult to tell," Yusuke commented.

"Meow?! I'm not telling anything!" Morgana snapped.

Seeing that they were done in the Jail, they all started towards the exit. With the exception of Ryuji, who was held back by Haru tapping his shoulder.

"What's up, Noir?"

Haru removed her hat and pulled him close. "That was a very sweet thing you did for Sophie." She lifted his mask and kissed him. "I'm lucky to have a man who's willing to defend his friends so readily."

Ryuji grinned dopily but couldn't find the words to reply.

~End of Chapter

Side note: In all honesty, the moment is still powerful even if Ryuji said fuck regularly in canon. Such a beautiful moment of pure friendship, I smiled so damn big when I saw that! I nearly cried!