Here is how the X-Men meet the sisters and tell their stories in X-Men in Equestria.
(we see Canterlot)
(Celestia is pacing her floor, sad that she was always alone in the daytime)
(a letter appears)
Princess Celestia:(opens and reads it)(becomes shocked)
(she runs to Luna's room, and knocks on her door)
Snowdrop: Mommy's not in there right now.
Princess Celestia: Well where is she?
[we see Hiro getting ice cream, and gives it to Luna and Yuna]
Yuna: This is the best day ever.
Skyla: You got that right.
(suddenly, Celestia appeared)
Shining Armor: Celestia, we didn't know you would be here.
Princess Celestia: There is a matter that we must attend to. Twilight has sent a letter of a crisis that went down.
Optimus Prime: What sort of crisis?
Princess Celestia: The Villains.
Starlight Glimmer:(walks up, pulling a cart of library books) The Villains were in Ponyville?!
Trixie: What else did the letter say?
Princess Celestia: The Diamond Dogs kidnapped the Crusaders and nearly got away with it, if one of Equestria's newest visitors hadn't intervened.
Princess Celestia: She called them humans with extraordinary powers.
Princess Luna: When do we meet these humans?
Princess Celestia: We leave right away.
(later, a chariot is flying to the town while some of the others traveled on the ground)
Princess Cadence:(raises an eyebrow) So what else did Twilight say?
Princess Celestia: She mentioned that one of them would meets us with them.
Yuna:(whispers to Snowdrop and Skyla) Who do you think it is?
Skyla:(whispers back) I don't know. I've never met them.
[Ponyville came into view and the Mane 6 and a hooded figure were waiting for]
Twilight Sparkle: That should be them.
Apocalypse: These princesses. What are they like?
[the chariot lands]
Princess Cadence: Twilight!(embraces her)
Twilight Sparkle and Princess Cadence: Sunshine, sunshine~
Clap your hooves and do a little shake~
Princess Celestia: Twilight, why have you called me here? Where is this visitor?
Apocalypse:(steps forward) I am he.
(they all turn to him)
Ironhide: Who are you supposed to be? And why are you hiding yourself in a hood and cloak?
[Apocalypse removes his hood]
Apocalypse: Shen, Elohim, Ra, Krishna, Yahweh. I've been called many names over many lifetimes. I am born of death. I was there to spark and fan the flame of man's awakening, to spin the wheel of civilization. And when the forest would grow rank and in need for clearing of a new growth...(in a deep, amplified voice) I was there to set it ablaze.
Ratchet: So you basically have the names of many gods.
Apocalypse: Yes, but I was born with one name - En Sabah Nur.