Go home...
"...Goodbye?" Lisa mumbled, staring towards the floor. "...Already?"
Professor Argall shook his head. "Lisa, wasn't this what you wanted?" He began, "What about your friends back in the simulations? What about everyone you've left behind?" He paused for a moment, staring down to his phone's screen. "You've made an amazing, beautiful world for everyone, Lisa. You deserve to experience it with the ones you love."
The girl glanced towards Samantha and Timothy. The former of whom continued to wreak havoc on her pancakes. "But I-- I'm not sure if I'm ready to go back yet. There's just so much that I want to learn about this world still..."
"Twilight, you have to go back. For Equestria." Timothy said, taking Lisa's hand. "C'mon. I know that I'll be going back now. Aren't you? Don't you want to see the rest of the girls again?"
Lisa sighed. "I don't know, Timothy. I just--"
"Twilight." The boy cut in, "Did you... did you just call me Timothy?"
Lisa groaned. "Spike, Spike. Yeah, I know... just, sorry, okay?" She turned towards her friend. "Samantha, you?"
"Please don't call me that again, Twilight." Samantha grumbled in return, the light in her eyes seemingly fading with each word. "I don't... I don't want to think about it anymore. It's fine coming from Argall, but from you... just don't. Okay? The Professor doesn't know, but you do. It's different coming from you."
"Say," Argall began, "I never got around to asking you about how things were going... uh, Pinkie, was it?"
Samantha nodded enthusiastically, flinging sticky bits of pancakes from her hair with each movement. "Yup! I've made it my goal to meet and make friends with everypony I meet! You should've seen Twily's face when I threw her a 'Welcome to Ponyville!' party! She was just all 'Waah!' and 'What?!' and stuff! Right? Remember that, Twi--"
"Woah there, girl." The Professor cut in, "I meant as far as the project. Lisa, erm... Twilight and I were discussing the days back when the two of you worked on the simulations yourselves. I just wanted to know if you'd like to talk about it."
Samantha shook her head. "N-nope!" She stammered, "Don't remember anything! I-I definitely don't... know... wh--what..."
Lisa pat her friend on the shoulder. "It's fine, Pinkie. You don't have to answer." She turned towards Professor Argall. "Sorry about that. She's kinda... touchy on that topic. It'd be best if we don't talk about it."
Another beep echoed through the room as the Professor immediately turned his gaze back to his phone.
"C'mon, Lisa. You're gonna miss the bus back to Snowbush if you don't go soon. I could come with you if you'd like. Just, y'know, talk over things one last time before you reconnect and all?"
Right... The girl thought, turning her attention to the brightly-lit windows, I've been living here in Mountain View for a while now, haven't I?
"Well, Twilight?" Timothy urged, tugging at the girl's hand, "Aren't you going? Pinkie's probably going to be there already by the time we're back. She'd probably throw us a 'Welcome Back to Equestria' party, even!"
Lisa sighed, laying her head on the table-- and her pancakes. "I'm not sure if I'll ever be ready to go back. I've grown to love my life in this reality just as much as Equestria. I don't want to give up either of them, not when there's so much to lose by choosing one or the other. This world is still so unfamiliar to me... even if I did originally live here-- there's so much more that I want to learn about. How did the world change while I was away in the simulations? What other simulations are there? Who is my real family? Yet, at the same time, I've still got everything that I know and love back in Equestria."
Timothy folded his arms. "So? What's so hard about choosing? We've always got things going on in Equestria as well, y'know." He turned his attention to Samantha. "Pinkie, what about you?"
Samantha shrugged. "Wherever Twilight goes, I guess. I don't want to miss out on anything fun that she might run into!"
Beep.
"We've got half an hour before the bus leaves with the other volunteers." Argall flatly stated, "Lisa, you've got to make up your mind soon."
"I..." The girl began reluctantly, "I have to go back to Equestria. For the sake of my friends."
The Professor eyed Lisa. "Are you sure?" He began, "I don't recall that you ever programmed in a way to leave the simulation from within, outside of in-simulation death."
"Yes." Lisa responded, regaining some composure, "I'm sure. I know my friends must be worried about me after being gone for so long. Pinkie?"
The upbeat girl glanced up from her last unfinished piece of pancake. "Yeah?"
"You ready to go back?"
"Y'know, Twilight..." Timothy chuckled, leaning his head against the frigid window of the bus, "If you told me a month ago that we were all actually humans and that Equestria wasn't actually real, I would've probably checked to see if you were Discord in disguise."
"Mmhmm." The girl turned away from Timothy, a sad look in her eyes.
Argall brushed past Lisa, practically falling into the seat behind the girl in a huff. "Well, Lisa. This is it, I guess. The final ride home for you, and a bus fare's worth of money out of my retirement savings for me..."
Whipping around to face the seat behind her, Lisa stared at her former mentor with a raised brow.
"...And the final moments I may ever have with one of the best students I could've ever asked for." The man finished, returning his student's stare. "Perhaps when you return to your simulation, I could code in an exit routine of some sort. You were in such a rush to get everything done and ready for release that you never remembered one of what I'd have to call the basic rules of life: Always find a stopping point, give yourself a break. You'll burn yourself out someday if you always make a rush for everything. There's a couple other simulations allow for their users to exit and enter at will anyways, so I can't imagine that it'd bring much harm if I add one to yours."
Lisa's eyes widened. "You mean--"
"As one of the founding members of what eventually became the network of Virtual-Realities that you call 'The Simulations', I have access to pretty much any part of the infrastructure including the very systems that run the simulations themselves." He smiled softly at the girl. "All I need is the permission of the lead developers of a simulated reality; That is, either your permission or Samantha's, and I would the be able to code in the exit code to let you connect and disconnect as you please."
The girl remained silent, staring in awe at her former mentor.
"Well, Twilight?" Timothy began, "Are you gonna let him?"
Lisa nodded, turning to Professor Argall with a wide grin. "Permission granted..." She confirmed, holding out a hand to the man. "...Starswirl."
"Noted." The Professor agreed, firmly shaking the girl's hand. "I'll get to it once I'm back."
Turning back towards the front of the bus, Lisa braced herself as the vehicle lurched forwards.
The bus fell into a dull silence for the rest of the trip, interrupted only by the sporadic thud of a pothole as Lisa once again slipped into unconsciousness.
Blinking, Twilight gasped as she found herself once again staring down the long aisles of books in her castle's library.
"Twilight?" A faraway voice echoed from beyond the door, "Twi-light! Where are you?"
The mare rushed to the door, tugging at the handles with her magic. "Right here! I'm right here!" She cried, grunting as she strained to open the unmoving fixture. "Can you hear me?"
The rushed sounds of hoofsteps filled her ears, growing louder by the second as the voice approached. "Girls!" The voice called out, clearer this time, "She's in here!"
"Help!" Twilight cried again, throwing her body against the door with a heavy clunk, "I can't get out!"
"Twilight, try teleporting!" Spike's voice yelled from behind the door, "Have you tried teleporting yet?"
The mare didn't answer, opting instead to channel her magic into teleportation. A bead of sweat rolled down her face as she strained to perform the spell in her panic.
"I don't think it's working, Spike." Rainbow's voice deadpanned, "Don'tcha think she'd be out here by now if it did?"
Twilight yelped in surprise as a bright light flashed from her horn, the spell backfiring and fizzling before her eyes. Choking from the ozone, the mare pounded on the door. "I can't!" She hollered, "It doesn't work!"
"Told ya." Rainbow's voice teased in response.
"Oh, stop it, darling." Rarity scolded the Pegasus, "Now's not the time for wisecracks."
The door rumbled for a moment as Applejack bucked the door.
A softer voice peeped through the door. "I'm sorry, Twilight." Fluttershy said, "If even Applejack can't get through, I doubt that anypony else would, outside of the Princesses. Even then, I'm not sure if even they can help, since you yourself couldn't get out..."
Twilight sank against the door in defeat, covering her face with her hooves. "Please..." She pleaded, "Get me out of this nightmare, please..."
A heavy wind gusted over the room, a flurry of papers fluttering about as books were thrown off the towering shelves. As the strange phenomenon died down, Twilight gazed up to find herself staring, once again, at Pinkamena.
"Shh..." The strange mare soothed, brushing a hoof over Twilight's mane, "It's gonna be okay, Twilight. You'll make it through. Shh..."
"P-Pinkie?" Twilight stammered, shuddering in the shadow of the mare, "Is that really you?"
"Not quite, Twilight..." Pinkamena answered softly, "Just close your eyes, and take a deep breath..."
The shadow over Twilight faded away, leaving no trace of Pinkie in its wake. The room had once again fallen silent, the voices behind the door all but vanished as the mare sat by the door-- alone.
"No, don't go!" Lisa cried, awaking with a deep gasp, "...O-oh... it was just... another... dream..."
The placid snore of the Professor sounded from the seat behind the girl, the sky since turning dark as the bus carried its passengers to their final destination.
"Hey." Timothy began, his eyes still closed as he leaned against the seat's headrest, "You alright there, Twilight?"
"Y-yeah..." The girl answered, staring out the frosted window, "I just... I just had another nightmare, that's all."
Timothy shrugged lazily. "Okay then." The boy yawned, turning over to lean his head back on the frigid window. "Wake me up when we get there."
Lisa sighed. I wonder how Equestria's doing... She thought, staring blankly ahead. It nearly feels like a lifetime since I've been there... She turned her attention to the empty rows of seats ahead of them, the only one occupied being taken by the other two Societal Management Officers that had volunteered to come.
Chad. The girl recalled, watching the short hair of the man shift over the seat. And that other girl... did I ever even ask for her name?
The darkened streets of Snowbush lay empty as Lisa said her goodbyes to the other Officers and Timothy, the latter of whom returned to his room as the other two wandered off into the moonlit street. Silently, the girl walked with Professor Argall along the unmarked path home.
Samantha... Lisa's thoughts turned to her friend. I wonder if she's reconnected yet?
She paused as another, more frightening thought entered her mind. She hadn't appeared to be anybody else besides Pinkie for the past couple days. What if-- The girl shook her head with a smirk. Nah... it couldn't be. That girl's more hardheaded than I could give her credit for.
"Eh? Something wrong, Lisa?" Professor Argall began, turning his head to the girl.
Lisa shook her head again. "It's nothing." She responded quietly, continuing on her walk. "Just a stray thought."
Even then... How long can she last fighting herself like that?
The heavy door creaked open, the girl and exhausted Professor entering the little house. Argall collapsed onto the cot, not giving a care to the metal handlebar protruding from the sides. "Finally." The man groaned, "I think I burnt more calories on that walk here than I have in the past month that I've spent at the gym..."
Lisa picked up a small, folded card taped to the console screen of the ever-whirring machine beside the cot.
"Instructions for reconnection" The card read. "READ ME"
The girl unfolded the card as the Professor sat up on the cot, brushing himself off. "Say," The man began, "You told me back then that you wanted to have your place isolated from the rest of the city. I don't think it has to be this far from society, y'know."
Lisa shrugged, reading the card. For a brief moment, her eyes brushed across her wristband-- something the girl hadn't noticed almost since the day she first woke.
"Lisa Garnet." The girl mouthed, turning her attention back to the card.
"The Pony-MeTM device communicates wirelessly via a BCI (Brain-Computer Interface) chip embedded in the subdermal layer of your head. This allows for easy and simple setup of the device, and streamlines the reconnection process for the end-user. To reconnect, simply fasten the Pony-MeTM headset firmly over your eyes, and when ready, answer the on-screen prompt with a verbal command to reconnect."
Lisa glanced towards the Professor, who had since vacated the cot and now leaned against the wall opposite to the cot.
"Go ahead." Professor Argall prompted, gazing at the girl with sad eyes. "It's your creation, your work. It's your reality, Lisa." He smirked one final time. "Or should I say, Twilight Sparkle."
Lisa nodded silently, acknowledging the old man's words as she slowly lay herself on the cot, her vision partially obscured by the loosely-fastened headset dangling above her eyes. With a resounding click, the headset snapped in place over her eyes with one final movement, and the world went dark.
Establishing connection. The words flashed before the girl's eyes. Please allow for up to a half an hour to complete the setup process. The nutritional supplement machine has been upgraded to an automatic process for the sake of convenience. Prepare for mild discomfort.
An airy whirr droned through the air as feeding tubes and miscellaneous cabling snaked under the railing, into the girl's side as they fastened with another click.
The girl's breathing slowed as a shot of anesthesia entered her body, the machine humming along as it set up the BCI.
Professor Argall turned to the girl one last time, a hand loosely gripping the brass doorknob.
"Goodbye, Lisa."
With one final thump of the door, the room was once again quiet, once again unmoving.
Wake up.
Take a look around.
The world is calling.
There's so much to see,
So much to hear.
There's new people to meet,
And old friends to greet.
You'll never know what's in store,
If you never open the door.
You have the power.
It's your choice.
Forge your own path,
Be your own guide.
The road is never smooth,
You are not alone.
More than what meets the eye,
There is always the unknown.
The truth may be hard,
Reassemble the puzzle.
Give it some thought.
The past never dies.
A brief glimpse is all it takes,
Now, there's a choice to make.
Go home...
Or go on...
Pony-MeTM
Ending 1
One ending down, more to go. There'll be an epilogue chapter following this one. Happy reading! 
Keep in mind that guest chapters are still open, and if you'd like, now would be a great time to add your own tidbit to the story. 
Anybody catch what's been going on with the chapter titles all this time?
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8895844
Now that chapter's finished. ^_^
OMNI:Dammit I was hoping some saints row Shit was going to happen ah well still a good story can't wait for the epilogue.
8898474
What was it that you had in mind specifically? Don't forget that guest chapters are still open, so if you'd like you could write an alternate endings yourself.
8898639
OMNI:The whole idea of finding loose bits of code that can be used to gain and upgrade abilitys,and I would write a geast chapter but all i have is my tablet.
Back Home. . .
Has Twilight not figured out that Samantha is stuck inside her own head, and Pinkie is keeping her there in a state of misery!? Am I the only one finding this whole thing horrifying?
Yes, I caught on to the chapter title thing.
If I was Lisa I would certainly be really annoyed with Timothy right now.
10395747
Heh. Yeah, that's one of the parts I'm likely cutting from this story's rewrite. Not that I've made any progress on it whatsoever yet. :P
No, what’s up with those titles?!
10574546
:)