Here is the scene where all natural disasters and the Time and Space rift are going out of control because too many Legendary Pokémon were here together fighting each other and Dark G-Merl's X-Blade in War of the Apocalypse.
(Suddenly an earthquake, tsunami and the lightning storm appears starts destroying everything in it's path)
Emerl: What's going on?!
Tino Tonitini: Natural disasters are going out of control!
Bonnie: How did this happened?!
Izzy Izumi: It's because too many Legendary Pokémon were here in one place and fight each other!
Lor McQuarrie: So that's why natural disasters are going out of control!
Sora: Now there are natural disasters and Time and Space rift all over the world! And it's going to destroy the entire world!
Laura: This is bad!
(Suddenly a bunch of tornadoes appears destroying every buildings)
G-Merl: Oh, great. Earthquakes, Tsunami and Lightning storm first. Then Tornadoes. What's next?
(Then Mt Fuji including volcanoes all over the world are erupting. Then a tsunami is flooding the whole city)
Emerl: Now volcanoes are erupting!
(Next there's a hail storm and blizzard freezing everything)
Ash Ketchum: It's cold!
Serena: Me too.
Ash Ketchum: Let me hold you to keep you warm.
Max Taylor: Now it's a hail storm and blizzard!
Yoshi: Brrr.... it's getting cold!
Dan Kuso: Very cold!
(Then a hurricane appears blowing everything in it's path)
Bebop: We are doomed!
Rocksteady: Let's get out of here comrade!
Galvatron: Let's get out of here!
(All the Villains retreat. Palkia fires Spacial Rend trying to stop the Tornado and it explodes getting rid of one of the tornadoes but more keeps coming back. Giratina fires Aura Sphere, Latios & Latias fires Dragon Pulse at another tornado, Articuno fires ice beam and Kyurem fires Ice Beam to freeze the tsunami)
Emerl: This is not good! More natural disasters keeps on going!
Alpha Gang: No! We're done for!
Runo Misaki: We're so gonna die!
(Dialga fires Roar of Time and Shiny Rayquaza fires Dragon Pulse trying to get rid of the clouds creating lightning storms be more of them keep coming back, then Primal Groudon stomps on the ground unleashing Precipice Blade to stop Earthquake and Tsunami)
Max Taylor: This is the end. All the terrible things that Princess Celestia warned us about. There happening, and the worst part is there's nothing we can do about it. We had our chance. But failed.
Zoe Drake: Oh, no!
G-Merl: How..... how could I've done this?
Mordecai: Don't you get it? It's the X-Blade! It's power is getting so strong it's gonna destroy everything, look!
(Lugia activates Whirlpool attack and Primal Kyogre smack the water with it's pectoral fin trying to stop the tsunami as well)
G-Merl: Darn it.... this is all my fault.... I should've turn into my evil dark form and use my evil X-Blade which causes natural disasters come.
Terra: That's the bad thing. First many Legendary Pokemon gathered in one place fighting each other, which causes Time and Space wrap appear on top of the sky. And then second, Dark G-Merl's X-Blade creates a powerful darkness which causes natural disasters to appear as well.
Rigby: Do something or we'll all gonna die!
Nighlock: (fires his Cosmic Eye Lasers to stop the Storms)
Scarlet Witch: (tries to hold back the earthquakes)
Vision: (fires his mind beam to stop the tsunami)
(we see Apocalypse and his remaining three Horsemen on a hill nearby, watching everything)
Magneto: This is what you meant, isn't? We left the villains, because this would happen?
Apocalypse: Yes. All the Legendary Pokemon did all the dirty work for us. Now, when the natural disasters destroy everything and everyone, we will build our new and better world.