Second idea
Miko, a glitch?
"...I just know that she's our friend," Five said, smiling softly at Miko.
"Thanks, buddy," Miko said just as gently, the gratitude for his belief in her clear in her eyes.
"But if you were a Glitch, you'd tell me," Five said to Miko as he leans towards her.
"Of course, partner," she said, smiling, although no one could see the slight guilt in her eyes.
(Some time later in the evening, Miko's house)
"Well, it really was a crazy day, wasn't it Miko?" Five asked her when the two of them were alone in their room playing some video games.
"Haha, yeah, really a crazy day," said Miko, clearly lacking the usual enthusiasm she usually has when gaming.
"I mean, sure, some glitches like Ally and Alpha obviously have some advanced artificial intelligence, and they understand quite a bit of what we say, but a glitch that can perfectly replicate a human? Even with the whole Budd thing, all the glitches were far from perfect," Five said as he continued playing the video game, not noticing how Miko was looking more and more gloomy.
"…" Miko remained silent and pretty much stopped playing herself.
"Um, Miko?" Five asked, finally noticing how his best friend remained silent and stopped playing.
However, Miko remained silent for the time being. She was deep in thought and felt great amounts of guilt, fear and indecision.
Even after all the words her best friend said to her and about her earlier that day, she still wasn't sure if he would continue to think of her that way if she told him. She has faith in her partner, but of all people it would hurt her the most if he rejected her once he knew the truth.
"Miko?" Five asked, standing in front of her, noticing that she seemed to be deep in thought.
Of course, she knows that Five would always be there for her no matter what, but what if she's wrong? What if he suddenly changes his mind once he learns that she is actually completely different than he thought? What if he gets mad that she's been lying to him the whole time and all his defenses towards her were actually for nothing?
"Miko," Five said, louder this time, and he waved his hand in front of her face, starting to worry about Miko.
What if he abandons her and reveals to everyone else that she's a Glitch?! What if he hunted them himself to get all the possible exp?! What if he hacked them, then reprogrammed them to take over first Hinobi, and then the world, ruling side by side and showing everyone what they could do as a team?! Wait, something was wrong, right?
"MIKO!" Five shouted very loudly.
It was then that Miko realized that she was lost in her thoughts the whole time and didn't notice her surroundings. Plus, Five's face is only a few inches away from her face.
"Waah," Miko screamed and jumped backwards.
"Miko! Is everything okay?!" Five asked his girlfriend worriedly.
"Ah, yeah, everything's okay," Miko said as she rubbed her head.
After that, both of them were silent for a bit, with Five continuing to look at Miko worriedly and Miko still looking down a little.
"Five, I, uh, should tell you something," Miko said slowly, still not looking up.
"What is it, Miko? "You can tell me anything, you know that. No matter what, I'll help you with whatever's bothering you, I promise," Five said to Miko, trying to calm her down.
"Five, I, earlier today, well, when we were all stuck together, I... I lied," Miko said quietly, trying to find the right words.
"What do you mean, Miko?" Five asked, not quite sure what she meant.
"When…when all of us were trying to figure out which one of us was a Glitch, then…I lied. Despite...despite what you and Inspector 7 said about it being impossible, that there is a glitch that can perfectly imitate a human, you are wrong. Because… because the truth is…" Miko tried to say, but she didn't know how to get the words out.
"Miko?" Five asked, confused and afraid.
"...I...I...I...I'M A GLITCH!" Miko shouted at the end.
Silence followed this statement. Werder Miko, who is on her hands and knees and looking down, says something, nor Five, who is kneeling himself, but upright, and staring at Miko with wide eyes.
Miko is quiet, having just revealed her biggest secret to Five. But although she is somewhat relieved to have finally told Five her secret, she is also very afraid of an answer.
Five, on the other hand, is quiet as he thinks. Or, actually, he's not really thinking, he's just trapped in his mind, with Miko's words repeating over and over as many scenes from the day and several of their adventures played out at the same time. Scenes in which she did something that is admittedly rather unusual and could rather indicate that she is actually not human but a glitch. Some of these scenes even feature Mitch previously listing all sorts of reasons why Miko is a glitch, but Five quickly brushes those particular thoughts aside as it's easy to see that Mitch is just jealous.
However, Miko is now thinking something like: "Why is this taking so long? Why doesn't he say anything?".
"I… I'm sorry I never said anything and I fooled you. I lied to you, I lied to everyone. You stood up for me like that earlier, and yet I tricked you all. I've been hiding who I really am, pretending to be something I'm not and now you know the truth and you're going to think just as badly of me as everyone else did and capture me and report me to Hinobi and hate me and... !", said Miko and began to sob in the middle of her monologue, but before she could continue, she suddenly felt two arms wrap around her and hug her gently.
It was Five who hugged her and held her tightly in his arms as he rested his head on her shoulder. No matter what his thoughts may be, he has to be there for his best friend right now.
"Hey, everything's fine, Miko. I don't really understand what you're telling me, but you're still my best friend, so calm down and start from the beginning. No matter what, I will always be there for you," Five Miko said, reassuring her a little.
Miko, hearing this, sheds a few more tears and continues to surrender to Five's embrace. It takes her a few more minutes before she begins to explain.
"I'm not actually human, I'm a glitch. I took human form about 16 years ago when I broke out of a computer program and have lived mostly as a normal person since then. The one who created the program was my mother, and after I escaped, she took me in as her own child. The only people who knew about it so far were she and my father, to whom she explained everything when she brought me home. And now you know it too. I never wanted to tell anyone, I shouldn't tell anyone, but you're my best friend and partner and we've already been through so much together and you mean so much to me and...!" Miko said everything and quickly started again speak, but Five interrupted again.
"Hey, it's okay, Miko. I mean, I'm really surprised, and I'm probably really tired so I'm not freaking out that much right now, but like I said, you are and will always be my best friend no matter what, so even if you're a glitch, "You are and will always be my miko," Five said, pulling back a little and placing his hands on her shoulders as he made her look at him.
Miko, seeing the sincerity in his eyes, begins to shed a few tears again, but this time out of joy. Her partner and best friend Hi-Five doesn't judge her for being a glitch and wants to continue to be with her.
"And don't worry, I'm obviously not telling anyone. "I understand why you want to keep this a secret, like just rely on me to support you through this," Five told her.
Miko then manages a smile and hugs him very tightly this time, nuzzling her cheek into his chest.
"Thank you, Five, really, thank you," Miko said very gratefully.
Five then hugged her back again.
Some time later both friends started gaming again, although Five still asked a few questions and Miko has no problem answering that it was Five.
Both friends knew that Miko's secret was something big, but neither of them let it stop them from continuing to be best friends and also best partners. Because like Five said, no matter what, the two of them would always remain friends and stay side by side together through thick and thin, no matter what.
Some time later, Miko and Five also told Miko's parents that Five now knew her secret, but although they both seemed a little upset about Miko telling her secret, her mother seemed smug for some reason and her father grumbled to himself for a while.
Second idea GT.