Here is how the Villains kidnap the Cutie Mark Crusaders, the X-men fight back, Apocalypse banishes Tirek, and Nighlock scares away the villains in X-Men in Equestria.
(we see the Diamond Dogs nab the Crusaders and stuff them in a bag)
(Scott is seen walking until he sees the kidnapping)
Scott Summers: Hey!
Diamond Dogs:(sees him and run)
Scott Summers:(chases them)
(we then see the villains waiting)
King Sombra: What's taking them so long?
Sonata Dusk: They're over there.(points them out)
(the Mane 6 come out, Applejack, Rainbow Dash, and Rarity looking angry)
Scott Summers:(catches up) Let them go!(takes off his glasses, and shoots his eye lasers at the Dogs, making them drop the bag)
(the dogs landed at the feet of Garble and his gang)
Tirek:(claps slowly) I've heard of humans being given rare abilities by others. But yours is powerful.
Scott Summer:(gets in front of the bag and puts his glasses on) You made a mistake coming here.(unties the bag)(to the Crusaders) Go.
Cutie Mark Crusaders:(runs for the crowd)
Evil Trixie: You're all alone. Loners are the weakest ones.(fires a magic blast that is redirected at her)
Sonata Dusk: What just happened?
Jean Grey:(walks into the open from the crowd)
Scott Summers: Hey Jean.
Jean Grey:(in Evil Trixie's mind) You never should've come here. You made the worst mistake taking the children.
Nightcrawler:(teleports around Sonata and beats her up)
Quicksilver:(runs around Gilda(Griffin) and rams Lightning Dust fastly) You didn't see that coming?
Jean Grey:(telepathically knocks out a few Changelings)
Aria Blaze: What happened to them?
Queen Chrysalis:(charges in anger)
Wolverine:(yells his war cry) RRRRRAAAAAHH!
(she looks up)
Wolverine:(slices off her wings)
Queen Chrysalis:(screams in pain)
Hank McCoy:(rips off her horn) RRRROOOOOAAAARRR!
Shadowcat:(arrives and takes down more Changelings)
Tirek: Enough of this! Sunset Shimmer, destroy them!
Clone Sunset Shimmer:(kicks Sombra in the face and does a split land)
Tirek: What is the meaning of this?!
Clone Sunset Shimmer:(shapeshifts into Tirek and smirks)
Evil Trixie: That's not Sunset, it's a Changeling traitor!
Quicksilver:(puts a pit in her face) The correct term is shapeshifter.(runs back to the team laughing)
Fake Tirek:(goes next to the team and shapeshifts into his true form, revealed to be Mystique)
Mystique: I thought you were stronger.
Tirek: That's it!(starts attacking innocent ponies)
(thunder is heard and lightning flashes)
Twilight Sparkle: Discord!
Discord: I'm not doing it. It may be unnatural, but I only do it on Saturdays and Sundays.(pulls out a calendar) And today's Wednesday.
(a lightning bolt shoots down and a woman wearing black and white hair stood there, with her eyes glowing white)
Diamond Tiara: Whoa! Who is that?
Sweetie Belle: I don't know DT. I don't know.
Silver Spoon: She rode lightning, for crying out loud. How'd she do That?
Quicksilver:(runs up next to them) She was born that way.
(a portal opens and Nighlock steps through)
Nighlock: I heard a party was happening in town square. I'm not late am I?
Scott Summers: In fact, we were just getting started.
(a blue force field appears and Nur steps out)
Apocalypse:(in Optimus Prime's voice) Taking the children, was a bad move.
Storm(X-Men):(creates a gust of wind and uses it to blow a wagon at Adagio)
Adagio Dazzle:(dodges it)
Nighlock: I like to let myself laugh at the funny things.(activates the armour's most powerful weapons - the Dybertronian cannons and sets them to blast)(in Rocket Racoon's voice) Like how much this is gonna hurt.
(the blast wipes out many of the Changelings, shocking Suri and the FlimFlam Brothers)
Tirek: You humans are all weak. Just because some of you have powers, doesn't make you stronger!
Apocalypse: Always the same.(in his amplified voice as he telekinetically blocks a magic blast from him) No more stones. No more spears. No more slings. No more bows. No more swords. No more!
Fluttershy: Um, why is his voice sounding like that's?
Applejack: And why do I feel like he's about to do something that's gonna surprise us all?
Apocalypse:(in amplified voice after sending a fire blast at Tirek) No more weapons! No systems!(normal voice) No more superpowers.
Tirek:(tries to stomp on him)
Apocalypse: You put so much faith in your tool...in your machines.(starts growing bigger and punches him)
Tirek: How is this possible?(pins him down)
Nighlock:(to Rainbow and Fluttershy) What's the weather supposed to be, today?
Rainbow Dash: Clear skies all day. Why?
Nighlock:(looks at Storm and smirks) Cause we could use a little storm right now.
Storm(X-Men):(smirks back and creates a whirlwind)
(Tirek starts losing balance and let's go of Nur)
Apocalypse:(gets up)(in amplified voice) You can fire your arrows from the Tower of Babel!(punches)
Scootaloo: What's the Tower of Babel? I've been there.(gets excited)
Scott Summers: It's an old legend back in our world.
Apocalypse:(body slams Tirek)(in amplified voice) But you can never... Strike... God!
(he then fires an energy blast which reverts Tirek to his weakest form and banishes him to Tartarus)
Apocalypse:(shrinks to normal size)
(Nighlock turns to the villains and flashes his Raven eyes at them)
(the villains run away)
Nighlock:(turns to everyone and crosses his arms in the form of an X) X!
(the ponies become confused, but Nur)
Apocalypse: Don't mind him, he does that a lot.