The Theory
"-our friends disappearing?" Rainbow Dash finished as she appeared in a large room with containers in it. "Where in the hay...?"
She slowly inspected each container to try getting clues to where she ended up. After a few minutes, Rainbow looked at one of the walls and saw things attached to it like nothing she had ever seen. There was a raised metal platform with five strange, identical sections resting vertically on top. At the top of them were round disks with what looked like mini green lightning bolts moving around.
What in Celestia's name is this stuff? Rainbow thought as she cautiously stepped onto the platform to inspect whatever this was.
"This some seriously freaky stuff and I need to get outta here," she said to herself as she noticed the door leading out of the room. The door opened automatically as soon as she was within a meter of it, spooking the normally confident pegasus, leading to a seemingly empty hallway.
Left or right? she thought as she turned her head from side to side. Too bad I don't have any bits with me to flip.
Rainbow Dash decided to go to the right. It really didn't matter since she had no idea where she was or where she was going.
"Intruder alert! Security to deck seven!" shouted a bald, blue-skinned being as he pointed a curved stick similar to what Pinkie had found earlier in the shuttle. "Stay where you are!"
Rainbow froze in her tracks, not knowing what the thing he was holding could do. A couple minutes later, two humans approached her from behind holding similar objects as the blue man.
"Ummm, what's going on?" Rainbow asked shakily.
"I'm afraid you're going to have to come with us," one of the other men said.
"Why? What did I do?" Rainbow inquired as she extended her wings in preparation of needing to escape.
Both of the men that answered the page of the first one replaced what Rainbow Dash could only assume were weapons back into holsters on their left hip.
"Crewman Chel, please holster your phaser and return to your duties," the other security guard said. "There doesn't seem to be any type of security risk with this horse."
Rainbow, clearly annoyed at being referred to as a horse, corrected him saying, "I am not a horse. I am a pony. Two completely different things."
"Our mistake," the first security officer said as Chel walked away. "Could you please come with us though?"
Rainbow flapped her wings to lift off the ground and hovered about shoulder height as the two humans with her.
"Where are we going?" asked Rainbow.
"To see Captain Janeway."
The two remaining ponies, Spike, Q and the Voyager away team had taken refuge from Celestia's sun inside The Castle Of The Two Sisters so that they could try formulating a plan to return everyone to their proper universes.
"So what exactly happened between you and Discord that caused a rift between our two worlds?" Twilight asked Q as he fashioned himself a chair from out of nowhere.
"Nothing happened," Q said innocently. "We talked to each other and we had our little strength contest. That's it."
"C'mon, Q. Details," Tom said flatly. "These ponies are the only way anyone is going home it seems."
"Well if you must know," said Q as teleported everyone back to the Delta Flyer and activated one of the consoles to show them the encounter
'What's this?' Q thought as he browsed through the different parts of the galaxy. 'A draconequus? I thought those were extinct.'
Snapping his fingers, Q created a shockwave that was able to get the attention of the mythical creature. In an instant, the serpentine being that was a mash-up of various animals appeared directly in front of the omnipotent being.
"Well, hello. Might I ask who and what you are?" said the draconequus.
"I am Q. And I am Q," answered Q.
"What?! That doesn't make any sense whatsoever."
"I'm a member of the Q Continuum which is comprised of hundreds of thousands omnipotent beings like myself," Q explained.
"Interesting. You and I seem to have the exact same voice. You wouldn't happen to be missing a member of the Q Continuum, would you?"
"No, I assure you that we are all accounted for," Q said.
"Oh, drat," said the draconequus as a box of tissues appeared from nowhere and he began to blow his nose and wipe his eyes as he made himself cry.
"Do you have a name or should I just call you draconequus?" Q asked.
The draconequus snapped his talon causing the tissues to disappear and become dressed in a top hat, dress shirt, dress coat, tie and carrying a formal cane in his paw. "Where ever are my manners?" He said as he took a bow. "I am the God of Chaos, Discord. The most powerful being in the universe."
Q took offense to Discord's claim of power and snapped his fingers intending to turn Discord into a mouse. What happened instead was Q himself was transformed into a single cell amoeba.
"Um, I should have told you... I can't be transformed into anything," Discord laughed as he watched Q squirm. "But seeing as though you are immortal like myself, I'll give you a claw." He snapped his talon and returned Q to his human form.
"My, my. That's a first," Q said humbly. "Someone that can actually deflect my power."
"Oh that's not all," Discord said with a huge smile.
"Really? What else can you do?" Q said as his smug attitude began to return.
"I can merge both of our universes together," Discord bluffed as he made himself appear as Shao Khan.
"Unlikely," Q said. "The only reason you're here is because the Q Continuum exists outside of the human realm. I brought you here."
"So if I set off some sort of magic explosion in here I could open a rift to another realm?" Discord said as he began channeling magic into his talon.
"The only thing that would happen would be a star going supernova in the human realm," Q replied confidently.
Discord snapped his talon again causing a beam of magic to fire toward the sky from his horns. Moments later an explosion occurred causing the stars from the Delta Quadrant to appear through a hole.
"Time to go exploring," Discord said as he disappeared while Q began to feel himself being drawn toward Discord's realm.
Q immediately realized that his powers had been reduced once he was completely into the alternate dimension. The window to the Continuum closed almost instantly and Q found himself trapped. In a desperate attempt to return to the human realm so he could get back to the Continuum, Q gave a snap of his fingers making a hole appear in the sky of this new planet. Somehow he was unable to escape through the rift no matter how many times he tried. After a dozen attempts he saw the Delta Flyer appear through the rift.
'There's a definite time differential between these worlds.' Q thought. 'There's no way that Janeway's crew detected this already. But I could use this as a way home.'
Q focused his power on the Delta Flyer a snapped his fingers.
The monitor then went black and Q transported everyone, except Rarity, back to their previous location. This did not go unnoticed by Twilight.
"Q, what happened to Rarity?" Twilight asked angrily.
"She was with us. I transported a dragon, two ponies, two humans, a vulcan, a hologram and myself," said Q.
"It is logical to assume that she disappeared to the same place the rest of the ponies have gone to, assuming they ended up in the same place," Tuvok said.
Rarity suddenly found herself in a large room containing three beds, a type of desk and an office off to the side. The walls had black panels similar to the ones in the Delta Flyer, however these had writing on them. Rarity walked around the room and found a cart that had various tools on them.
I wonder if any of these could protect me, she thought as she attempted to levitate one of the items. Why won't my magic work? I guess I'll have to take my chances then."
Rarity walked out of the room and began to wander the hallway outside.
"So what exactly does the Delta Flyer use to fly?" Twilight asked Tom.
"The power supply is run off of electromagnetic plasma," Seven replied first. "There emergency systems that are on now have battery packs that will run for approximately 72 hours."
"Electromagnetic plasma? As in electricity?" Spike asked.
"Yes, quite similar," Tuvok said.
Twilight rubbed her left hoof back and forth against her chin in deep thought. Suddenly her eyes shot open as an idea popped into her head.
"Would do you think that lightning might be able to give it enough power to at least fly toward the rift Q made?" she asked excitedly.
"It may be possible to fuse the battery packs to the warp core so that we can use the power from the batteries and from the lightning strikes," Tuvok said.
"You said 'strikes'. How many do you think will be needed?" Twilight asked as her voice changed from excitement to worry.
"We would have to scan the strength of the lightning first to determine the specific amount," said Seven.
"What about when we do get the Flyer off the ground," Tom asked with his arms crossed. "If we get to the rift, it's going to pull us right back here."
Q finally joined the conversation after a few minutes of listening. He had partially created this mess and felt compelled to assist in fixing it.
"What about the ponies and your friend Discord that were pulled into the other universe?" he asked with a raised eyebrow. "How are they going to get back?"
"Good point," Tom agreed disappointedly. "If we get through, the rift will more than likely close."
"Has anyone tried making contact with Voyager since we've been here?" asked the doctor. "If the ponies are somehow going to Voyager, why not see if we can send a message?"
"That's a great idea!" Twilight said with a big smile on her face. "If you can talk to your crewmates, we can-"
"Twilight!! No!!" Spike shouted.
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Ok, I'm gonna sound like a total nerd, but I don't think Q is technically named Q. If I recall correctly, he always introduces himself by saying 'I am Q.' That having been said, it might be funny if you changed his reply to Discord's two-part question to: 'I am Q. And I am Q." But then I'm not sure if that would fit Q's sense of humor.
/nerd
Anyway I'm really enjoying this so far! I'm not much of a Trekkie, but I really did enjoy Voyager. I feel like it had more... heart than TNG, in general.
8412500
That actually has a better ring to it.
Hmm, using lightning to recharge the warp core? I sure hope they remember to recalibrate the flux capacitor or they end up God knows where... or when
Come to think of it... couldn't Celestia just lift Delta Flyer off the ground and throw it through rift? She can move the entire sun, so space shuttle should be a piece of cake...
By the way - did Rarity end up in Chakotay's quarters?
8413087 Rarity ended up in the empty sickbay. I haven't decided yet if Twilight should appear in Janeway's Ready Room or Engineering.
Edit: Stay tuned for an interesting final chapter...
8413109
Ah dang, I missed the 'three beds' part somehow... thanks for clarification
Twilight in the engineering? Hmm, knowing her, she would probably start asking Vorik or someone about 'what is this and what is that...' pissing B'Elanna off, in no time... could be fun
8413129 Pissing B'lanna off? Considering Discord got smacked around earlier, it definitely sounds fun...
8413145
I can imagine Twilight talking with Vorik with B'Elanna nearby, asking him about every single panel. After a few 'Oh, this is fascinating!' comments from Twilight followed by a few Vulcan 'indeeds,' B'Elanna would probably want her out of there...
B'Elanna: 'I want you out of here now!'
Twilight: 'But I haven't completed studying that equipment yet...'
B'Elanna: 'Study this: pony provokes Klingon. Klingon makes pony into soup!'
OK, that was somewhat paraphrased from one of the episodes, but still
8413180 Ok. Now I need to binge-watch Voyager to see which episode that's from.
8413209
If you want to start from the beginning, then it might take a while since it is at the end of season 5
'Someone to Watch Over Me' - to be exact.
8413250 Thanks.
I cannot figure out how this paragraph should be rephrased XD
Btw, the first "The" should most likely be removed.
maybe change the last part to "why not send a message?"
8413760
Thanks once again. That first error was written on my lunch break at two in the morning and the second was about four in the morning battling insomnia.
8413250 I can't believe I missed that scene. Especially with it being that early in the episode.
8412500
Actually in several episodes he refers to himself and other members of the Q Continuum as "Q". In the episode Death Wish, the Q discovered is called "Quinn" (for simplicity's sake) but refers to Q as Q.
Later, Q's son (played by John D. Lancie's son--that was kewl
) was called the same though spelled as "q". 
8451084 I think you misunderstood. All the Q are called Q... but they're not individually named Q. Their 'species' is named Q. And they refer to each other as Q. But they never, to my knowledge, introduce themselves by saying 'My name is Q.' It's always 'I am Q.' That's a big distinction.
8451292
Yeah, and I don't think I've ever said, in my entire life, "My name is Wacky". I just say, "I am Wacky" or "I'm Wacky".
My example points out that one Q called another member of the Continuum "Q". Meaning they get something that we, a lesser race of just humans, can't. That's the name he goes by and that's good enough for me.
Hope you continue this. Thanks for the good read.
8713261 I do plan to finish it. Just a few other things to take care of first.