"huh? It must be something.... Oh. That was where I stood during the spell"
"Ok, you need to stand vertically." Jeremy asks Twilight. "I'm sorry if that's uncomfortable, but the scanners are designed for bipeds. I only need to do this the first time. Please stand up."
A pause from Twilight as she (Slightly unstably) stands on her hind legs. "Ready!"
Twilight Sparkle explodes purple pixels, leaving behind a wire frame that fades away.
~****~
Twilight didn't know what to expect from 'Earth'. Whatever it was, it wasn't what happened. First off, she was in a cylinder. That must be why I had to stand vertically Twilight thinks to herself. Second, she notices she has a magic bubble from some source that isn't her. Who could be giving her safety? Third, her Eye of X.A.N.A "Cutie Mark" (it's not really, CM manipulation can't make it so you have two different CMs) is glowing bright white, then have most of it fade to black.
"huh? It must be something.... Oh. That was where I stood during the spell"
~****~
"WHAT JUST HAPPENED? Jeremy, YOU BETTER EXPLAIN THIS S#!T" RD yells, thinking Jeremy just KILLED TWILIGHT.
"Dash, calm down. She'll speak with you now." Jeremy responds in a panic.
"How? You just wiped her from existence!"
"Not quite."
~****~
Twilight notices the doors of the scanner open. "Twilight! Convince your friend that I didn't kill you!" Jeremy calls out.
"How?" Twilight asks.
"Just tell him... ooops her what happened. Just speak into that mic."
Twilight walks up to the mic. "RD, can you hear me?"
~****~
"RD, can you hear me?" Rainbow can't believe it. That was Twilight Sparkle!
"Wait. WHY AREN'T YOU DEAD?" RD calls out in confusion.
"I just entered another universe. You're all 'inside' this machine called The Supercalculator. I just was 'Devirtualized'. What this entails is that I don't die, but I can't renter 'Lyoko' for 12 hours." Twilight takes a deep breath. "Does that make any bucking, sense?"
"Language, Twilight!" Rarity says. Twilight expects her to take out the couch, but she doesn't.
"I guess... except no, not at all." Rainbow Dash says confused.
"I'll have to look into how to explain that better."
~****~
"Jeremy, I know something is up. There is a girl in the lab, and it's not Yumi or Aelita." Will asks Jeremy.
"Oh s#*t. I'm going to tell you the truth, but it's going to sound like a lie. A purple unicorn pegasus hybrid is trying to convince her friends that she is safe. Who are still in Lyoko. In a new version of The Forest Sector." Jeremy panicked.
"I have never heard a more blatant lie since you told me the Supercalculator was completely safe." Will remarked
"I never told you that. That's a lie and you know it. So, you want to prove me wrong? Let's enter the lab."Jeremy opens the doors in a less dramatic that you would expect fashion, given that there is talking pony inside.
"Dash, I can't come back right now. There is a 12 hour timeout. Do you really think it's a good idea to at-" Twilight Sparkle says, then notices the people enter the room. "Hold on, Dash. There is some people that I think need to talk to me." She takes off the headset (It does not fit over her ears, so the volume was quite high). "Hello, who are you?"
"Jeremy, have you been messing with Code: Earth again?" Will asks.
"Kind of. But these just kind of appeared into Lyoko along with The Everfree Sector and The Crystal Sector." Jeremy pauses. "She is also one of the six new members of our team."
"WHAT??!! You know you need unanimous vote to elect new members of our team!"
"You're forgetting that we all agreed to change it to majority vote."
"Well f$%k."
"You still haven't told me your names. Who is the sta- I mean man and who is the woman?" Twilight speaks up.
"Terribly sorry, purple pegasus with a horn. My name is William Dunbar." William says.
"Oh! I must have forgot to say my name. I am Twilight ... Victoria Sparkle. It's normal to have a middle name, right? Because I just kind of made it up. Nice to meet you Will. And you are.... "Twilight points her hoof at Aelita.
"Umm... I'm Aelita Schaeffer. I didn't know there was other intelligent beings in Lyoko."
"'Other'? You mean you were stuck in that place too? We can talk when the rest are out." She then opens up the Supercalculator manual to the Code: Earth segment, reads a bit, then proceeds to devirtualize Dash. This surprises the f*#k out of the Lyoko Warriors. Not just that she could understand that dence as s#*t manual, but that she levitated the manual.
"How did you do that?" Will asks out of astonishment.
"I just looked thur-" Twilight starts, then is cut off by Will.
"No, how did you levitate a book?"
"Magic."
"How did you really do it?"
"I cast a.... Oh right. Magic free universe. I shouldn't expect you to understand magic."
"So we now have six 'ponies' that look like they're from MLP. I don't know if I should barf right now."
"What is MLP?" Twilight sighs."I have a lot of research ahead of me"
Suddenly, the scanner doors open, revealing RD."Hey, is one of my cutie marks glowing and then looking like this normal?" 
RD asks.
Opening the door to the lab, RD asks "Whoa, are these people? They look cr-"
"Stop that. They could have killed us!" Twilight replies, shoving her hoof into Rainbow's mouth. "And yes, it does appear to be normal. We seem to have a mark based on where we were during the crossover spell."
"Wait. You came via spell? I'm so confused." Ulrich says, coming out of a different scanner.
"I know you enter using this scanner, that must take care of the fancy spell for you."
Everyone else is just kind of stuck wondering whether to facepalm or look really confused. Hint: they choose option two.
"I'll just go over and devirtualize the Lyoko Warriors now and not ask questions." Jeremy finally manages to say.
"Sounds like a plan." Aelita awkwardly adds.
~****~
"Sorry for the delay guys. Yumi, Odd and Ulrich, prepare for devirtualization." Jeremy says.
"Who would have thought devirtualizating PONIES would have caused a few problems? Also, Ulrich is already devirtualized." Yumi deadpans.
"Oh, must be the monitor glitching up. I'll just devirtualize Fluttershy as well. Devirtualizating in three...
Two...
One..." Jeremy calls out. The Lyoko Warriors explode blue pixels, leaving behind a wire frame that fades away. Fluttershy explodes purple pixels, leaving behind a wire frame that fades away.
~****~
"Eep! What's happening to one of my CMs?" Fluttershy says, one of her CM's looks like this:
The scanner doors open, and Fluttershy returned to her normal, four legged stance. Odd notices Fluttershy standing on her four hooves."Oh wow, I didn't think you were actually Fluttershy!.... I shouldn't be so hyper about this. I know how poorly you deal with fame." Odd facepalms. "... I just dug myself deeper, didn't I?"
"EEEEP! How do you know that?"
"I freaking called it. If anypony knows why the elements of harmony have there own TV show here, it would be Twilight Victoria Sparkle."
"I have so many questions right now, but I'll put them off until later."
"Same here." Yumi says.
~****~
"Ok, that just leaves you three. Rarity, Pinkie Pie and AJ" Jeremy says. "Get in position for devirtualization."
"Will do!" Pinkie Pie chirps as she jumps up on hind legs like it was nothing.
"Ah'm ready." AJ says as she carefully gets up on her hind legs.
"If I must." Rarity says as she gracefully moves to a bipedal position.
Jeremy devirtualizes the three ponies.
~****~
"Huh, what is that?" Rarity says noticing the change in one of her cutie marks. 
"I don't remember it looking like that before."
"Ah'm sure my Cutie mark had something to do with apples. Both of them, that is." AJ says, noting that one of her Cutie marks now looks like this:
"Hey! We're now live action! I didn't even know that was possible! My actor looks just like me!" Pinkie Pie says, then notices her changed Cutie mark. 
"They got that part wrong though."
"Ok, I think I just maxed out my weirdness limit." Ulrich says, noticing the two other ponies in the lab.
"Wow. If you think you maxed out your weirdness limit, Pinkie Pie will break the scale." Twilight remarks.
Will facepalms. "That's her name? Really?"
"Her name is actually Pinknemea Diane Pie, but we use her nickname." Twilight Victoria Sparkle replies.
Will facepalms again for good measure. "Are you f%&king kidding me? She is Diane. Pinkie Pie is the worst name ever."
Suddenly, Pinkie Pie pops out from behind the computer terminal, even though the lab door never opened.
Yumi says one word. "wat."
"If you value your sanity, DON'T QUESTION HOW SHE CAN DO THAT. Believe me, I've tried." Twilight says.
"Said the pegasus unicorn combo." Ulrich deadpans.
"It's called an alicorn! Use the right terminology!" Odd says, irritated.
"Are you kidding me right now? Odd, the boy who dated every girl in the eighth grade except Aelita and Sissi, is into My Little Pony? ................. don't mind me, I just need to REBOOT MY SENSE OF REALITY." William says.
The lab door opens, revealing AJ and Rarity. "Ah'm sure she went in here, Rares." AJ says as she bucks open the door (carefully, so she doesn't take it off it's hinges).
"Darling, I don't think that's the best way to open a door. Just use your forehoof." Rarity pauses as she notices everyone in the room. "I apologise for my entrance. I should learn all of your names. By the way, thanks for 'devirtualizing' me. I wouldn't want to be stuck in that monster infested hellhole."
Pinkie pie gets excited by her friends entering the room. "Now that we're all here, LETS SET UP A PARTY!" she pulls her party cannon out from behind her back. "I'll just fire this and make a party. This place is a little too small though. Is there someplace bigger?"
Twilight quickly interjects. "Remember. DON'T QUESTION IT."
"Oh. Ok....." Jeremy mutters. "We can go through the boiler room to go to the factory floor. that should be large enough."
"Oki Doki Loki!" Pinkie Pie says as she runs through the boiler room. An explosion sound is heard from above, then she comes back down to the lab to say "The party is ready!"
"I severely doubt that." Yumi says as she walks through the boiler room. As she opens the door to the factory floor, she has to swallow her words. "Oh. HOW DOES A CANNON MAKE A PARTY?"
Twilight speaks up, reminding her "If you value your sanity, DON'T QUESTION HOW SHE CAN DO THAT."
She begins to head back though the boiler room, saying "Whatever, it just means she doesn't have to spend forever getting the party ready" She returns to tell them. "Go see for yourself."
Needless to say, everyone was quite surprised to see that a cannon could set the factory floor up for a party. Everyone and everypony decided to start partying and have a great time. Except for Twilight Sparkle, who is in the lab, digging for info on earth, MLP, the Supercalculator and magic.
This doesn't bode well for either the party or the research.
Some intense partying and research later...
Twilight runs up the stairs. "Hey! I have got all the info you need!"
"Ahnd then ya'll join the party right?" AJ asks.
"Yes, I will. I think you should sit down for this." Twilight says, right before she starts her explanation.
Her explanation.
"So, as you all know, we seem to have another, different cutie mark that wasn't there before. I have determined that it is, in fact, not a CM. It is a marking of X.A.N.A. who is keeping us alive. This may sound off, given that it was just trying to kill us. The reason is that ehXANA is doing this is that it is pro-magic. It was created to defeat Project Carthanage, which puts a damper on the Supercalculator's magic."
"Wait just one moment. I thought there was no such thing as magic in this world!" Yumi interjects. "Also, you pronounce it XANA."
Twilight continues with "Well, it's not very prevalent. The team working on the Supercalculator found out how to do it. That's how the attacks XANA does works and how return to the past works. XANA was born from Waldo Franz Schaeffer's desire for a magical world. He went mad while working on it, and it shows in it's actions. Cue Project Carnage. Carthage was developed to stop XANA from exerting the extreme magical power of the Supercalculator. However, it has breaks and issues. These manifest themselves in Lyoko as towers."
"I'm sorry, I didn't catch that. Most likely because I was distracted by the fact A MAGICAL, TALKING PONY told it to me."
Ulrich says.
Twilight blushes. "I-I'm sorry. I-I can't help it." She then continues, but is cut off.
"Wait. Project Carnage was built before the supercomputer." Jeremy interjects.
Twilight facehoofs. "Oops. What I meant to say is that it was modified and placed in the Supercalculator. Anyway, the only way XANA can get passed the barrier of Project Carthage is by activating a tower or keeping someone alive because of it. This is because of the "Preservation of life" exemption. XANA has grabbed on to it twice, once with Aelita and the second time with us. If XANA stopped, which it can do, it would lose the opening, and kill the person or pony. However, if the being died for a reason other than that, the opening would stay open, leaving XANA with unrestricted control of the power."
"So, if any of you die on earth it's Game Over?" Odd asks.
"This is new. Odd, when did you start paying attention to lectures?" Yumi asks, surprised.
"Ever since they were given by Twilight Sparkle." Odd replies.
"I guess." Yumi replies.
"Let me see here...." Twilight says, flipping through an imaginary filling system. "Yes, I suppose it would be 'Game Over'. For the world. All three of them. Equestria, Lyoko and Earth. Anyway, XANA's ultimate goal is to defeat Project Carthage and kill all humans so he can remake the world with more magic. No idea where he got that idea."
"Ahre ya done there?" AJ asks.
"Let me think.... yes I am. Let's party!" Twilight says.
------------END OF EPISODE!----------