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 Gyarados with 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 Pokémon 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 Pokémon (Charizard and Absol respectively), with Alain noticing the Mega Stone on Absol's necklace. The two Pokémon immediately begin to fight, with Charizard using Flamethrower, which is countered by Absol's Psycho Cut. Absol then lunges at Charizard with a Megahorn, which Charizard 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 Pokémon, then cause a flash when Charizard's Steel Wing collides with Absol's Megahorn. Meanwhile, Mairin is playing with her Chespin, Chespie, 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 Pokémon, and marvels at how strange these Pokémon seem. After exchanging blows with Mega Charizard, Mega Absol charges with a Psycho Cut, which Mega Charizard stops, and wins the battle with a powerful Blast Burn. Both Pokémon revert to their normal forms and Astrid congratulates Alain on his win, asking him if fighting Mega Evolutions is all he does. Alain responds that he wishes to defeat all Mega Evolutions, and have Charizard stand at the top.
Alain later sits with Charizard by a river and ponders the strength of Astrid's Mega Evolution, then calls out Mairin, knowing she is hiding behind a nearby bush. She comes out, and after asking a bunch of questions about Mega Evolution, reveals she is a novice trainer who just received a Pokémon from Professor Sycamore. As she asks him about Mega Evolution, Alain has a flashback about learning about Mega Evolution with Professor Sycamore, and asking him if he and Charmander could go on a journey together. After being jolted back to reality by Mairin, Alain receives a call from an unknown man telling him to check out ruins, and as he leaves Mairin follows him.
Alain goes into the ruins and finds a Mega Stone (most resembling Gyaradosite although it is unconfirmed). As he leaves he is confronted by Remo and his Garchomp Garchoo. Remo challenges Alain to a battle for the Mega Stone, to which Alain accepts. Both Charizard and Garchomp Mega Evolve and engage in an aerial battle, to which Charizard comes out victorious.
As Alain and Mairin walk along a path, they encounter a Flabébé, which Mairin engages in a battle, catching it, and nicknaming it Bébé.
Alain meets Siebold at the restaurant, and challenges him to a battle. Alain Mega Evolves early and starts fighting Siebold, with Siebold's Blastoise holding its own even without Mega Evolving. Siebold finally Mega Evolves Blastoise and both Pokemon engage in a fierce battle, with Blastoise finally coming out on top. Siebold congratulates Alain on his power while Alain concedes defeat. Alain then sets off with Mairin on a quest to discover Mega Evolution.
The final scene portrays a man (the un-introduced Lysandre) staring at a bunch of charts, presumably graphs measuring the power of Mega Evolution.
- The episode continues with Pokémon: Mega Evolution Special II.