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As Satoshi and his friends continue their journey, they stop by some wetlands. Incredibly, it turns out this is Numelgon's old home. Numelgon is overjoyed to be reunited with its old friends, but it appears to act a little odd. As it turns out, these wetlands have been the site of a strife between Pokémon over who gets to live there. As Satoshi and his friends are surprised to learn Numelgon's past, an army led by a Florges shows up and attacks! In order to protect its friends and the peace of its homeland, Numelgon stands up and prepares to fight!
Satoshi and his friends visit the Platane Laboratories. They are delighted to learn that the Mega Stone Professor Platane has found is a Gabliasnite, but then the Key Stone, the Mega Stone and Gablias get stolen by the Rocket Gang. Satoshi and the others chase after the Rocket Gang as they flee the scene, but the Rocket Gang attempt to mega evolve Gablias and send it to attack them!?
The Miare Gym match is finally here, and it is time for two men to fulfill their promise to each other! Satoshi and Citron have traveled together up until this point. This battle between two who know each other's characteristic traits, such as the Pokémon they use and the moves they prefer, extremely well is bound to be more intense than any other! The two clash against each other with all they've got... Which Pokémon will be the one to hold the final key to victory...?
Having returned to Miare City, Satoshi has reunited with Citron. But just as they are about to start the Gym match they promised each other, Junsa suddenly appears, saying she's come to arrest the Citroid. It appears that a robot that looks just like the Citroid has been committing various acts of mischief. Satoshi and the others start an investigation to prove the Citroid's innocence.
As Satoshi and his friends head towards Miare City, they reunite with Tierno in a forest. But during a training battle against Tierno as preparation for the Gym match, one of the Rocket Gang's mechs show up and abduct Tierno's Kameil and Raichu and Satoshi's Numeil. Satoshi and the other manage to find the Rocket Gang, but trouble arises when a fire breaks out during the resulting battle. But then, a certain Pokémon stands up to save everyone!!
Satoshi and his party are walking along a road going through a forest when they come across the Evolution Pokémon Eievui, which has been tied to a tree trunk and left behind together with trays containing food and water. While at first glance it seems it's been abandoned like an unwanted dog, the Eievui has a tag around its neck engraved with the name and address of its Trainer, reading "Taichi, No. 14, district 3, Stone Town". The group checks their map and see that Stone Town is the city just ahead of them.
Thus, Satoshi and the others decide to bring the Eievui to this address. When they arrive at no. 14, district 3 of Stone Town, they find that it is a massive house that puts even a Beverly Hills mansion to shame. They can also hear cheering and applause coming from within. Can the Eievui's Trainer be found here at this mansion?
NOTE: As mentioned in the Pocket Monsters 39 release post, this episode was the second part of the show's 1 hour re-premiere special and was originally meant to be the 41st episode of the series, following "Cyber Soldier Porygon", "Rougela's Christmas" and "An Iwark Bivouac" in that order. From this point on, the upcoming episodes would be aired in the order they were intended to be aired in for a while.
The story thus far: Alan travels around with his partner Lizardon in order to fulfill his goal of mastering Mega Evolution and stand on top as the strongest. With the newbie Trainer Manon in tow, he participates in Mega Evolution battles in all kinds of places. The two of them encounter Champion Daigo in the Houen region and decide to search for the legendary megalith together with him. But then, Rayquaza suddenly appears. Alan and Daigo fight it, but it ends up just disappearing.
Alan continues his journey to master Mega Evolution and stand on the top as the strongest. Together with Daigo, he pursues the legendary megalith that disappeared together with Mega Rayquaza. During this search, he receives information that Groudon has suddenly appeared in the sea. Alan and the others hurry to the location in question, where not only Groudon appears before them, but Kyogre as well. Furthermore, Rayquaza descends from the heavens and a grand battle between the legendary trio begins! What will this mean for Hoenn's future!? Will Alan and the others even survive this!?