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（アクトワン）～ Pocket Monsters XY Special Episode: The Strongest Mega Evolution ~Act II~) is an episode that is a part of the short anime special series, Mega Evolution Acts and a sequel to Mega Evolution I.
Alain continues his journey to find and defeat all of the Mega Evolutions in the world. He next meets up with Hoenn Region Champion Steven Stone, who has also been travelling to understand the secrets of the Mega Stones, but both are caught off guard when Rayquaza appears in the skies.
An excavation team digs out a wooden slab, on which is written that a giant stone exists, supposedly the stone is an origin of Mega Evolution. Alain and Mairin, however, have arrived to Hoenn region via the airplane. Later, Mairin and Chespie hurry up and run, while Alain finds a trace of a Mega Stone. Suddenly, Mairin cries out for help, as she got her butt stuck on a bush. She is helped by a man, whom Mairin thanks for help. The man introduces himself as Steven, welcoming Mairin to Hoenn region. Alain and Chespie arrive and Mairin introduces them to Steven. Alain bows, but notices a Key Stone on Steven's jacket. Alain asks Steven for a battle, since he wants to defeat all Mega Evolved Pokémon, but Steven replies he is busy. Alain reminds him eye contact means a challenge to a battle, so Steven decides to battle for a short moment.
Alain sends Charizard, against Steven's shiny Metagross, who possesses the Mega Stone. Mairin remembers steel-type Pokémon are weak against fire-type attacks. Alain presses his Key Stone, Mega Evolving Charizard. Mega Charizard uses Flamethrower, but Metagross uses Psychic, redirecting the attack towards the sky. Steven presses his Key Stone, Mega Evolving Metagross. Mega Metagross uses Flash Cannon, hitting Mega Charizard, reducing its speed. Alain plans on finishing the battle quickly, having Mega Charizard hit Mega Metagross with Dragon Claw. Mega Metagross retaliates with Meteor Mash, sending Mega Charizard onto a rock, since Mega Metagross' speed has increased. Mega Charizard breaks out and returns to the battlefield, attacking Mega Metagross with Blast Burn, but after the smoke clears, Mega Metagross is still standing. Steven reminds Alain not to underestimate Mega Metagross. Mega Charizard uses Dragon Claw and clashes with Mega Metagross' Meteor Mash, but the attacks are interrupted by a Flamethower.
A Pyroar appears, surprising Alain and Steven. A man with red hair appears, which Alain calls as the director. Per director's orders, the battle is stopped and both Pokémon revert to their original forms. The director apologizes for Alain's rudeness to a battle challenge, knowing Steven is the Champion of Hoenn Pokémon League. Mairin hears the director's voice, as the director introduces himself as Lysandre, owner of the Lysandre Labs in Kalos region, who asked Alain to investigate the Mega Evolution. Mairin asks Lysandre did he contact Alain some of the time. Lysandre asks Alain who is this girl, so Mairin introduces herself to Lysandre, as she travels with Alain. Lysandre thinks Alain has a small girlfriend, making Alain surprised. Mairin clarifies she is no girlfriend of Alain, who asks her to move away, for he has things to discuss with Lysandre. Mairin feels insulted, but falls down, to the bush again. Steven asks Lysandre what did he mean by "investigate" Mega Evolution. Lysandre replies his Labs are collecting data about Mega Evolution from Alain's battles, hoping some peaceful purposes can be achieved from it.
As Lysandre shows Steven the slab, Mairin asks who Lysandre is. Alain replies he is an important person to him. Alain was searching for the Mega Stone for Charizard, who, back then, evolved into a Charmeleon. While searching the ruins, he was approached by Lysandre, who showed him an Ampharosite. Alain battled for the Mega Stone, using Charmeleon against Pyroar, but lost. Lysandre replied to achieve greatness, Alain has to become the strongest. However, Lysandre let Alain come to his mansion and told he is seeking ways to use Mega Evolution. Alain advised Prof. Sycamore can help him, but Lysandre avoided that, since Sycamore may publish the info, causing bad people to claim such data and misuse it. Lysandre told the professor must be protected, as he showed Alain the Key Stone and the Charizardite. At the present, Mairin has Alain come to his senses, as they follow Lysandre and Steven.
They come to an excavation site, where they meet up with Steven. Steven admits he has been researching some stones, but seeing the Mega Stones, he has been working to uncover its origins. Steven shows them a wooden slab on his tablet, which is what brought Lysandre and his disciples here. Lysandre shows a holograph of a wooden slab, but with different text, since the original slab was broken into pieces. Steven knows if they were to bring the pieces together, they will find the answer. Steven reads "the path to the megalith starts with the gate", while Lysandre continues "the key to opening the gate is a glimmer of two stones - when those two stones come together, a new path will appear". Steven is certain the text refers the Key Stones. They climb up the tower, finding two pillars, which represent the gate. Alain and Steven touch the pillars, their Key Stones responding, as a shining bridge leads towards the mountain. Steven is grateful for Lysandre, for they couldn't accomplish this without his text, as well as Alain for participating in this. Mairin thinks Alain is important to have the Champion's gratitude.
They climb the shining stairs and find come to the ruins of the megalith. Steven reads an ancient text and has Alain go to the other altar. They show the Key Stones close to the altar, which reacts in a shining light. The center reacts, summoning the megalith. They think that is the origin of Mega Evolution, as Alain's Key Stone pulses. Lysandre sends word to his people, claiming they found it. An airplane appears, as Lysandre has his scientists set the equipment to analyze this megalith. The megalith starts pulsing, as the scientists discover this megalith, while being similar to the Mega Stones, radiates a much greater power. Suddenly, the sky turns dark, for a Rayquaza appears. Rayquaza links itself to the megalith and Mega Evolves, starting to roar, which awakens a Groudon and a Kyogre. Mega Rayquaza fires out an attack, blowing the ruins up and destroying the airplane. Lysandre wonders if they enraged Rayquaza. Alain sends Charizard and immediately Mega Evolves it, along with Steven's Metagross.
Mega Charizard uses Flamethrower, but Mega Rayquaza dodges and attacks Mega Charizard. Mega Rayquaza uses Dragon Ascent, hitting Mega Charizard. Mega Metagross catches Mega Charizard, but is attacked as well. Mega Rayquaza uses Draco Meteor, damaging the ruins. Mairin tries to escape, but nearly gets hit, so Alain saves her. Steven wonders if Mega Rayquaza wants to destroy the place. The megalith starts responding and explodes, causing Mega Rayquaza to fly off. Steven removes the rubble and notices Alain and Mairin. Alain holds his shoulder and while he claims he is fine, Mairin knows he is lying. At any rate, the megalith is gone, as they all wonder if it is connected to Mega Rayquaza, who is above the planet and reverts to its original form. Lysandre detected some energy waves at Rustboro City, sensing they are the same ones from the megalith. Lysandre claims they will find the megalith back, dismissing Alain to Rustboro City. Steven decides to find a transport for there. Before leaving, Alain is ordered by Lysandre not to leave the Champion, for his knowledge is useful to them.
The humanity tries to understand the Mega Evolution, but such knowledge can bring many changes to humans and Pokémon, as many more forms of Mega Pokémon are uncovered.
- Mega Beedrill
- Mega Pidgeot
- Mega Slowbro
- Mega Steelix
- Mega Sceptile
- Mega Swampert
- Mega Sableye
- Mega Sharpedo
- Mega Camerupt
- Mega Altaria
- Mega Glalie
- Mega Salamence
- Mega Metagross (Steven's)
- Mega Latias
- Mega Latios
- Mega Rayquaza
- Mega Lopunny
- Mega Gallade
- Mega Audino
- Pyroar (Lysandre's)
- The sequel takes place in Hoenn compared to the previous one which took place in Kalos.
- The special continues with Pokémon: Mega Evolution Special III.