Here is the scene where Nightmare Moon unleash the Black T-Rex command it to destroy the heroes and the city as well. Then the Black T-Rex gets defeated by the fusion move and the Mane 6 use the elements of harmony Nightmare Moon turning her back to Princess Luna in War of the Apocalypse.
Nightmare Moon: I'm glad you can make it, heroes!
Tino Tonitini: Why are you here!?
Nightmare Moon: Just to help the Villains to destroy you! Black T-Rex arise!
(Her eyes glows and a red beam pops out of the ground summoning the Black T-Rex and roars)
Nightmare Moon: Now Black T-Rex! Destroy them!
Max Taylor: We're gonna use our dinosaurs to fight the Black T-Rex!
Zoe Drake: Yeah! We defeat that Black T-Rex once and will do it again!
D-Team: Dino Slash!
A-Team: Alpha Slash!
(Chomp, Ace, Paris, Terry, Spiny and Tank grow into full size Dinosaurs)
Rex Owen: We need more Dinosaurs!
Zoe Drake: Pass up the cards!
(Rex gives more dinosaur cards to Dr. Z and Zoe gives more dinosaur cards to Laura and Rod)
Rod: Thanks Zoe.
Max Taylor: Let's do this!
D-Team: Dino Slash!
A-Team: Alpha Slash!
(They slash every cards together summoning an army of dinosaurs facing the Black T-Rex)
Nightmare Moon: (Laughing Evilly) You think your army of Dinosaurs can defeat me and the Black T-Rex?!
Dr. Z: Oh yes, they will defeat the Black T-Rex!
Nightmare Moon: Then I'll send you fools and your dinosaurs to extinction!
Krog: I Don't think so!
Kamzo: You're going down!
(Tino transforms into his half pony form)
(Just then Rod's Latios and Laura's Latias shows up)
Rod & Laura: Take down that Black T-Rex!
Tino Tonitini: Let's dance!!!
Black T-Rex: ROOOOOOOOOOOOOOAAAAAAAAR!!!!!!
(They all fight the Black T-Rex)
(Tino tries to attack it with his keyblade but it hits him with his tail. Next Latios and Latias fire Dragon Pulse together but it's too powerful and hits them away)
Tino Tonitini: That dinosaur is tough.
Nightmare Moon: Your next!
(Nightmare Moon unleash the attack trying to kill Tino, but Twilight's force field blocks the attack and saves Tino)
Tino Tonitini: Thanks, Twilight.
Twilight Sparkle: You're welcome.
(Tino gets out his keyblade and then fights the Black T-Rex)
Tino Tonitini: You wannta piece of me!? Try to get me!!
(Black T-Rex tries to step on Tino but he moves away as it steps on the street)
Tino Tonitini: You missed!
Nightmare Moon: Oh, really?
(Nightmare Moon teleports and came of nowhere and hits Tino)
Max Taylor: Tino!
(Nightmare Moon hits Max)
Rex, Zoe, Rod & Laura: Max!
(Nightmare Moon came of nowhere and blast the members away and laughs)
Zoe Drake: Where did she go?
Dr. Z: Show yourself, Nightmare Moon!
(Nightmare Moon fire her magic and hits the D-Team and A-Team)
Nightmare Moon: It's all over.
(Twilight Sparkle attacks Nightmare Moon, but then Black T-Rex hits Twilight with it's tail knocking her away into the small store)
Rainbow Dash: Twilight!
Nightmare Moon: I've been waiting a long time for this.
(Just then Princess Celestia arrives)
Princess Celestia: That's enough Nightmare Moon! You must come back to me as Princess Luna!
Nightmare Moon: Princess Luna. Is nothing but a bad memory of yours, Princess of the sun!
(Just then the two Princesses fight each other. During the fight Nightmare Moon fires her magic and hits Princess Celestia and falls down)
Twilight Sparkle: Celestia!
Tino, D-Team & A-Team: Princess Celestia!
Nightmare Moon: (Laughing Evilly) It is all over now! The night will last forever! (Continues laughing evilly)
Tino Tonitini: (Getting furious) I'll make you pay you monsters!
Max Taylor: Looks like it's time for our revenge! Fusion move style!
D-Team & A-Team: Right!
(Everyone slash the move cards and the army of dinosaurs unleash their attacks together creating a fusion move. As the Black T-Rex unleash fire scorcher it hits the fusion move but it's too strong and hits the Black T-Rex)
Max Taylor: Yes!
Black T-Rex: RRRROOOOOAAAARRR!!!!!!
Zoe Drake: Oh, no!
Rex Owen: Looks like it's still standing. Two more hits might do it.
(Cut to Tino, Mane 6 and Nightmare Moon)
Twilight Sparkle: You'll never get away with this, Nightmare Moon!
Nightmare Moon: I am getting away with it now!
Applejack: It's payback time!
Rainbow Dash: Yeah, you'll be so sorry!
Nightmare Moon: I'll kill you all!
Tino Tonitini: Oh, boy.
(Cut to the Black T-Rex gets hit by the fusion move)
Dr. Z: Take that!
Max Taylor: One more hit, then it's finished.
(Cut back to Nightmare Moon fighting the heroes)
Tino Tonitini: We can't give up! We want you back Princess of the night!
Twilight Sparkle: We know you're in there, Luna.
Nightmare Moon: Silence!
(She fires her magic)
(Cut back to the Black T-Rex gets hits by the fusion move for the last time and then finally gets destroyed as the D-Team and the A-Team cheers in victory)
(Cut back to Mane 6 using the elements of harmony)
Twilight Sparkle: Ready.
Applejack, Rainbow Dash, Pinkie Pie, Rarity & Fluttershy: Ready!
Rainbow Dash: Loyalty!
Pinkie Pie: Laughter!
Twilight Sparkle: Magic!
Nightmare Moon: (Scared) No. no.
(They activate their elements and crests and unleash the rainbow beam and then hits Nightmare Moon)
Nightmare Moon: NOOOOOOOOOOO!!!!!!!!!!
(A light of explosion explodes as the screen fades to white and then fades away)
Twilight Sparkle: Princess Luna?
Princess Luna: What happened?
Tino Tonitini: Tirek uses his dark spell to turn you into Nightmare Moon.
Max Taylor: Tino!
(The D-Team & the A-Team run to them)
Laura: Luna! Your back!
Princess Luna: That's right. Thank you all so much.
Zoe Drake: Welcome back, Princess Luna.
(Then Twilight Sparkle helps Princess Celestia to get up on her feet but she gets up by herself)
Princess Celestia: I'm okay. (Walks to Luna) My dear sister. I'm so glad you're back.
Princess Luna: I'm so happy to see you too.
(Princess Celestia and Luna hug each other)
Twilight Sparkle: We've got to stop the Villains and free all Legendary Pokémon.
Tino Tonitini: You're right, let's go!
(They run off)