Here is how the X-Men wake up in Equestria and the villains plan their revenge in X-Men in Equestria.
(we see eyes open and hear Hank's voice)
Hank McCoy: Logan? Logan, can you hear me? Come on Logan, wake up.
Wolverine:(opens his eyes)
Hank McCoy: Oh, good, you're awake.
Wolverine: Where are we?
Hank McCoy: We are in a cottage. If we can just find out who owns it, we can ask them to help us find the others.
Wolverine:(sniffs the air) We're in luck. She's just now returning.
Hank McCoy: Oh.
(they go down and sit on the couch)
(the door opens and reveals a yellow pegasus with a pink mane that fell slightly over one of her eyes and a pink tail)
Wolverine: I see you're the shy type.
Fluttershy:(looks over to her couch and sees them) Oh good, you two are awake.
Hank McCoy: Greeting young one. Hank McCoy.(holds out his hand for her to shake)
Fluttershy: I'm Fluttershy.
Wolverine: I'm Logan. I'm the best there is at what I do. And what I do, isn't very nice.
Fluttershy: Oh my. Your cuts and bruises aren't there anymore.
Wolverine: What cuts and bruises?(realizes it) Yeah, they're not there anymore, because I heal faster than normal people.
Hank McCoy: Anyways, could you help us find our friends? We got separated after one of Forge's experiments failed.
Fluttershy: Of course.
(they leave the cottage)
(we see Jean Grey wake up in a colorful room)
Pinkie Pie: Hi!
Jean Grey:(yelps in fear) Where did you come from?!
Pinkie Pie: From the door silly. I'm-
Jean Grey: Pinkie Pie. Yeah, your thoughts are running around my head.
Pinkie Pie: You can read minds? That is so awesome!
Jean Grey:(telekinetically gets her away from her)
(meanwhile, Shadowcat was waking up as well)
Shadowcat:(to herself) What happened? Where am I?
Spike: You're in Twilight's castle in Equestria.
Shadowcat:(sees Spike and phases through the bed in shock)
Spike: Whoa, how did you just do that?!
Shadowcat: I was born with that ability. What are you?
Spike: I am a ferocious fire breathing dragon!(flexes his muscles)
Shadowcat:(rolls her eyes) You look like a baby dragon to me.
(Spike's muscles deflate)
???: Spike! I told you not to disturb our guest until she wakes up!
Spike: But Twilight, she is awake! Come see for yourself!
[a purple pony with a horn and wings walks in]
Shadowcat:(to herself outloud) Between evil mutant brotherhoods, mutant killing robots, and mutants with godlike powers, this one takes the cake.
Twilight Sparkle: What are you talking about?
Spike: Twilight! You wouldn't believe what she did when I saw here wake up.
Twilight Sparkle: And I thought I told you to not mess with her until she woke up. What were you doing in her room?
Spike: Well, you also said Starlight was late again, so I went to find her. She still hasn't found her way around this place, remember?
Twilight Sparkle: Oh right.
Thomas:(whistles and pulls up) Hey guys what's up?
Twilight Sparkle: Hold on Thomas. Spike, what can she do.
Spike: She fell through the bed, like it wasn't even there!
(meanwhile, Storm was waking up in what looked like a tree house)
Zecora: Fell from the sky, some say you did. But fixed you up, i did in a jiff.
(someone knocked on the door)
Zecora:(sighs) Wait here one moment, while I let in these people.
(when she opened the door, two strange men were standing there)
Storm(X-Men): Anthony, Nur, how did you find me? How did you get here?
Nighlock:(takes off his sunglasses) We went through the portal. The only way to stop it from destroying Earth, was to close it from the inside.
Storm(X-Men): So we're trapped here?
Apocalypse: We're mutants, Ororo. We'll figure something out.
(we then cut to Quicksilver waking up and standing on clouds)
Quicksilver: Wait clouds?(sees he isn't falling through)
Rainbow Dash: How are you doing that?!
Quicksilver: Huh, guess it's because of my powers.
Rainbow Dash: What powers? Twilight said that humans don't have powers.
Quicksilver:(runs out of the room at a fast speed and back in with two sodas)
Rainbow Dash: How did you do that?!
Quicksilver: I was born this way. How else? Can we please get on the ground?
Rainbow Dash: Ok. Cody is somewhere here.
(later, we see Mystique wake up and hear voices talking from a distance)
???: I say we get their attention by taking the Crusaders.
???: You and your hatred for Rarity. Rainbow Dash humiliated us.
???: Either way, revenge will be ours.
Mystique:(in her head) Not on my watch.(kidnaps and ties down one of the villains) I'll need your form.(shapeshifts into Evil Sunset Shimmer)
(in Sweet Apple Acres)
(we hear voices telling Scott to wake up)
Scott Summers: Where am I?
Applejack: Well, mah Granny wants you to open your eyes so she can check them.
Scott Summers: Where are my glasses?
Granny Smith: You'll get them when I check your eyes!
Scott Summers: Trust me, that's a bad idea.
Granny Smith:(looks at Big Mac)
Big Macintosh:(opens them)
(as soon as Big Mac opened Scott's eyes, a laser beam shot out of them, blowing a hole in the roof)
Scott Summers: See what I mean?(closes them)
Applejack: We cahn ya're point.(hands him his glasses)