Plot of the special revolves around the young man Alain. He has Charizard as his partner just like Red. Alain's main focus is very different from other trainers. Unlike other trainers, Alain doesn't take part in leagues or Gym battles. Instead he want to master the Mega Evolutions. He wants to know which Mega Evolution is the strongest.
The story starts off with a brief battle between a Mega Abomasnow and Mega Gyarados facing off in the rain beside two unknown trainers. Mega Gyarados unleashes a Hydro Pump, which is then frozen by the Mega Abomasnow, who then runs toward the Mega Gyaradoswith their final clash of two Hyper Beams creating a flash, and leading the narrator to begin talking about Mega Evolution.
The narrator talks Mega Evolution, explaining how it makes a Pokemon stronger and more magnificent looking, though not much else is currently known about it, all while every single Mega Evolution is displayed in the background.
After the title is shown, the story flashes to a clearing in the middle of the forest, where Astrid and Alain stand along with Alain's Charizard. Astrid is surprised to see that on a metal collar, Charizard is wearing a Mega Stone. Alain acknowledges that they are both strong trainers, and that it is time to prove it, causing Astrid to laugh and ask his name. Alain and Astrid both introduce themselves, and send out their Pokemon (Charizard and Absol respectively), with Alain noticing the Mega Stone on Absol's necklace. The two Pokemon immediately begin to fight, with Charizard using Flamethrower, which is countered by Absol's Psycho Cut. Absol then lunges at Charizard with a Megahorn, whichCharizard simply stops by grabbing its horn. Alain then admits that Astrid is powerful, but that he knows she can do better. They both activate their Mega Rings, causing both Absol and Charizard to Mega Evolve. They both compliment each other's Pokemon, then cause a flash when Charizard's Steel Wing collides with Absol's Megahorn. Meanwhile, Mairin is playing with her Chespin, Chespi, when she falls into the river as a result of Alain and Astrid's battle, causing her to go and investigate. She then sees the fight between the two Pokemon, and marvels at how strange these Pokemon seem
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- The episode continues with Pokémon: Mega Evolution Special II.