"Pokémon: Mega Evolution Special III" serves as the third installment in the Mega Evolution Special series, continuing the narrative centered on Alain, a skilled Pokémon Trainer and researcher specializing in Mega Evolution. The story builds on the events of the previous specials, delving deeper into Alain's quest to understand the mysteries of Mega Evolution and his growing conflict with the enigmatic organization, Team Flare.

Alain, accompanied by his Mega Charizard X, is driven by a desire to uncover the true potential of Mega Evolution. His journey intersects with Ash Ketchum and his friends, who are traveling through the Kalos region. The narrative explores Alain's internal struggle as he grapples with his motivations and the ethical implications of his research. His alliance with Lysandre, the leader of Team Flare, becomes increasingly complicated as Alain begins to question the organization's true intentions.

The plot intensifies as Team Flare's plans to harness the power of Mega Evolution for their own agenda come to light. Alain is forced to confront the consequences of his actions, particularly his role in aiding Lysandre's experiments. The story highlights key battles, including Alain's encounters with powerful opponents, showcasing his growth as a Trainer and his evolving relationship with Charizard.

The special also introduces key characters such as Mairin, Alain's young companion, and her Chespin, who provide emotional depth to the narrative. Mairin's unwavering support and optimism contrast with Alain's more reserved and conflicted demeanor, adding layers to their dynamic. The interactions between Alain, Ash, and their respective Pokémon further emphasize themes of camaraderie and rivalry.

As the story progresses, the stakes rise with the introduction of the Legendary Pokémon Zygarde, whose power becomes central to Team Flare's ambitions. The climax of the special sets the stage for the larger conflict in the Pokémon XY&Z series, with Alain's choices and alliances playing a pivotal role in the unfolding events. The narrative concludes with a sense of unresolved tension, leaving viewers anticipating the next developments in the overarching storyline.