In the middle of a lunch break, our heroes are happily surprised by the appearance of their old friend Sanpei and his Greninja. They’re heading home to Ninja Village, and our heroes are invited!
There they meet Sanpei’s brothers, Ippei and Nihei, as well as the village chief Hanzo and his assistant Shinobu. All are impressed with Sanpei’s growth as a ninja and a Trainer. Our heroes marvel at all the amazing Pokémon there...and Team Rocket, watching from above, plots to catch them all.
Out of nowhere, several Skarmory attack the village, and a group of masked ninja abducts Chief Hanzo! Who are they, and what are their intentions? The answers to come, as the journey continues!
At Kagetomo's headquarters, he discusses his plans to invade Hanzo's Ninja Village. The Ninja Corp, with its leader Heidayu, swear their allegiance to Kagetomo.
Elsewhere, Ash has finished training with Frogadier and is preparing to have lunch. Squishy senses a foreign presence nearby, and Frogadier soon also senses something amiss. Frogadier then launches off its frubbles, blocking an incoming attack. It is revealed to be Sanpei and his Greninja, and Sanpei compliments Frogadier on having noticed their presence. Serena invites Sanpei for lunch and he accepts. Over lunch, he explains that he had been on his way home to the Ninja Village to be part of tomorrow's village festival. As the group express their interest in coming to the village, Sanpei happily invites them over. Bonnie then dresses as a ninja with a pink ninja outfit made by Serena.
The group, along with Sanpei, enters a cave which appears to be a dead-end. Sanpei proceeds to knock on the stone at the end of the cave, with a man answering with the word "mountain". Sanpei replies with the code "river", causing the stone door to slide away, revealing a path. Sanpei is greeted by two men who tell Sanpei that everyone will be happy when they see him. The path then leads the group to Ninja Village, a town encased by cliffs on all sides. Sanpei greets the villagers, and the word eventually gets to his brothers, Ippei and Nihei. His brothers come to greet Sanpei, and compliment Sanpei on evolving his Frogadier. Hanzo, the village chief, along with Shinobu then greet the group. After laughing too hard, Hanzo begins to cough in exhaustion, and is taken care of by Shinobu. Hanzo then begins to flirt with Shinobu, only to reveal that Shinobu had performed a ninja body switch on Hanzo. Bonnie asks her to be Clemont's "keeper", but Shinobu reveals that she is in fact much older than she looks.
Nihei then challenges Sanpei to a battle to see how much he had grown. Nihei calls out Venusaur, and proceeds to use Vine Whip after Sanpei's Greninja had used Double Team. The battle then continues, but despite Greninja landing a sneak Night Slash, Venusaur overpowers Greninja by concealing itself with a Petal Blizzard and finishing off with a Solar Beam. Hanzo then comments that Sanpei had left too many openings and could have won with his first Night Slash. Ippei reveals that Venusaur had blocked that Night Slash within moments of impact. However, despite the loss, Hanzo and Ippei compliment that Sanpei had grown since last time.
Elsewhere, Kagetomo has defeated a villager protecting the village outskirts. He then lauches a Skarmory army to attack the village.
Ash and the group are now exploring the caves which serve as homes for the villagers and follow Sanpei to his room. Ash's Frogadier notices a photo in his room, showing Sanpei with his Froakie before he had left on his journey. After Clemont asks Sanpei what he plans to do next, Sanpei replies he will stay at the village to train and help his brothers as Ippei will soon be made the next village chief. As Sanpei is talking, Dedenne is playing around with Squishy, but accidentally falls down a hidden trap door in the floor. Bonnie notes their absence and Sanpei reveals the trap door, thinking that they may have fallen through to the secret underground passageways. Bonnie and an unwilling Clemont follow through, and the rest also decide to go through the trap door as well. At the other end, the falling Dedenne and Squishy are caught by Nihei, while Bonnie's fall is stopped by Ippei. The others then enter the passageway with a smooth landing, with the exception of Clemont, who falls flat on the ground, and Serena, who ends up on Clemont's back.
Sanpei's brothers then lead the group to a monument dedicated to the hero of the village, a Greninja. Ippei tells them the story related to the hero, back when the village ninjas had fought against each other. While the reason for the fight was unknown, the Pokémon of the village had defended their village, with Greninja as their leader. Ippei and Sanpei reveal that they had chosen Froakie as their starter in admiration of the hero. Bonnie then comments that the Greninja in the picture looks different to ones she had seen before.
Meanwhile, Team Rocket have been spying on the village and begin to plan on stealing the village's Pokémon. They plan to create a ruckus to lure out all the villagers' Pokémon, and then capture them using their devices. However, before they could do so, Kagetomo's Skarmory fleet closes in to attack the village. As the villagers flee, alarms warn Ash and the group underground of danger. Ippei suggests that Sanpei take Ash and the group to Hanzo while Ippei and Nihei investigate outside.
Ash and the group arrive at Hanzo's place, however, they are soon followed by the entrance of Kagetomo and his ninja corp. By creating smoke, they capture Hanzo and flee. Sanpei and Ash follow, but as Serena is about to follow, Shinobu stops her since it would be too dangerous. Shinobu instead tells Serena to find Ippei together.
Outside, Ippei and Nihei are continuing to defend the village from the Skarmory. Team Rocket, still in their Meowth balloon, then plan to use the ruckus already made for them to steal the village Pokémon. Jessie throws a capture device at the Pokémon, but the device becomes knocked off by Skarmory's attack. It instead lands next to Shinobu and Serena who are running towards Ippei, binding the two together.
Elsewhere, Ash and Sanpei continue to chase Kagetomo, but are stopped by Heidayu and his Bisharp.