Pokémon: Mega Evolution Special II (Japanese: ポケットモンスターXY特別編 最強メガシンカ ～Act II～Pocket Monsters XY Special Episode: The Strongest Mega Evolution ~Act II~) is the second Mega Evolution Special and the third special episode of the XY series. It first aired in Japan on November 6, 2014 (just after XY049) and in the United States on February 7, 2015.
Alain and Mairin, along with their partners Charizard and Chespie, have just arrived in the Hoenn region as they continue their quest to unravel the mysteries of Mega Evolution. It isn’t long before they encounter another Trainer named Steven, and Alain can’t resist challenging him to a Pokémon battle. Steven unleashes his Metagross, who has the ability to Mega Evolve just like Charizard!
The exciting battle is interrupted when a Pyroar bursts onto the scene. It’s soon followed by its Trainer, Alain’s boss Lysandre, who owns Lysandre Labs in the Kalos region. He’s interested in collaborating with Steven, the Champion of the Hoenn region, to research the power of Mega Evolution and to harness that power for peaceful means.
Together, the group travels to an ancient ruin where Lysandre and Steven combine their research to discover a massive, glowing Giant Rock that resembles an immense Key Stone. Lysandre calls in his team of scientists via helicopter to begin studying their find, but their activities summon Rayquaza from the sky. Unexpectedly, this Legendary Pokémon Mega Evolves—without the help of a Trainer—and begins to attack the ruins!
Mega Charizard X and Mega Metagross battle back, but Mega Rayquaza launches a massive attack and flies away. In the aftermath, the group is surprised to see that the Giant Rock is missing. Based on Lysandre’s readings, he sends Alain to Rustboro City to track it down, and Steven and Mairin come along for the journey!
Landing in Hoenn, Alain and Mairin walk down a foggy mountain. The duo encounter Steven Stone, whom Alain challenges in a Mega Evolution battle. Steven accepts, taking out his Metagross. The two Mega Evolve their Pokémon, and fight a worthy battle. While Mega Metagross and Mega Charizard X are about to finish each other off, a Pyroar unleashes a Flamethrower and interrupts the two. The Pokémon belonged to Lysandre, a businessman who owns a lab in the Kalos region. He is revealed to be Alain's boss, and Alain tries to shut Mairin out of his affairs. In a flashback, Alain contacted Professor Sycamore about Charmander's evolution to Charmeleon. He was trying to find a Charizardite in some ruins and encounters Lysandre, who proposes him a deal: a Charizardite in exchange for his help. Before leaving, he tells Alain that he has to be the strongest. Back in the present, Alain and Mairin follow Lysandre and Steven up to Mt. Pyre.
Steven reveals that he traveled in search of stones as he was interested in Mega Evolution. He and Lysandre show to each other two different wooden tablets. One half shows the location of the gate and the other half shows the way to open it: a Mega Stone. Both Trainers take one pillar, revealing a stairway that leads to the mountain. At the top, they find some ruins in search of the Giant Rock. Steven and Alain find two daises and activate them, revealing a crystal.
The group finally finds the Giant Rock. Lysandre talks in his communicator, and a helicopter flies in. A science team starts researching the power of the Giant Rock, and in the process the sky turns dark, and Rayquaza appears. A sudden glow engulfs it, and it Mega Evolves into Mega Rayquaza, awakening Groudon and Kyogre. Mega Rayquaza is in a rage, destroying everything in its path. Alain and Steven take out and Mega Evolve their Charizard and Metagross. Mega Charizard X fails to use Flamethrower against Rayquaza, and Metagross fails to attack as well, and Rayquaza counters with Draco Meteor. It then flies away. The ruins are destroyed, Alain is injured, and the Giant Rock is gone. With Rayquaza on the loose, Lysandre instructs Alain and Mairin to head to Rustboro City and investigate there, with Steven tagging along. In secret, he instructs Alain to stay close to the Champion, as his knowledge of Mega Evolution may prove to be useful.
Because Steven is stated by Lysandre to be the Hoenn Champion, it is implied that, at some point, he had taken the title from Wallace, who was stated in Our Cup Runneth Over! to be the Champion of Hoenn.