During our heroes' journey to Cyllage City, Ash and Froakie meet a young ninja named Sanpei and his Frogadier. Ash challenges them to a battle, and Frogadier defeats Froakie with an impressive Quick Attack. Sanpei is about to take his leave when Ash asks him for some special training. He’s never seen anything like Frogadier's Quick Attack, and he wants Sanpei to teach Froakie how it’s done!
Sanpei agrees, and Froakie enters ninja training. Thanks to Serena's costume skills, Bonnie, Dedenne, and Pikachu get to play ninja too! Sanpei takes Froakie through a series of exercises designed to increase its speed, including chasing Frogadier as it jumps swiftly from rock to rock, leaping through the trees at an incredible pace, even moving its feet fast enough to run on water. As the drills conclude, Froakie is finally ready to try its own Quick Attack.
Just then, their training is interrupted by Jessie, James, and Meowth, who have grand plans to nab Froakie and Frogadier and form their own ninja Pokémon squad for Team Rocket. They manage to net Frogadier and Pikachu, but Froakie is just too quick for them—so quick, in fact, that it creates an illusion of being in many places at once. This unexpected Double Team attack overwhelms the villains and sends them blasting off again!
With all the Pokémon safely returned, Sanpei thanks our heroes for saving Frogadier. Ash reminds him that without his generous training regimen, Froakie wouldn't have acquired the skills that allowed it to rescue Frogadier. And so, saying their goodbyes, our heroes once again hit the road for Cyllage City, site of Ash’s next Gym battle!
Along a road, Ash and Froakie are training. While Ash is satisfied with the results, a stranger from the trees is not. Froakie shoots its frubbles at a tree, and the stranger, having been disguised to blend in with the tree, reveals himself, a ninja. As Ash and his friends exclaim, the ninja uses his "ninja leaf shroud" technique to suddenly vanish. Froakie notices rustling in a bush, and when it shoots its frubbles, they are shot back, the work of a Frogadier. The ninja boy introduces himself as Sanpei. Ash takes the opportunity to have a battle, and Sanpei complies, after concerns that Froakie was lacking in strength. Froakie begins with Bubble, followed by Pound repeatedly, both of which Frogadier evades with its superior speed. Once realizing his disadvantage, Ash commands Froakie to use Water Pulse, but is deterred by Frogadier's Smokescreen, and the ninja's Pokémon temporarily vanishes. Ash commands Froakie to find Frogadier's position and use Water Pulse again, but Froakie hits a decoy made by Frogadier, who jumps from behind it. Sanpei orders Frogadier to use Bubble and Water Pulse, and Froakie counters with the same attacks for both but is overpowered. Frogadier counters Froakie's final Water Pulse with Quick Attack, and Froakie is hit, dodging too slow. As Sanpei uses a final Quick Attack to finish the battle, he realizes the Froakie cannot fight back and moves the Pokémon out of danger with his leaf shroud trick. The battle is over, and Ash has lost.
As he tends to Froakie, Ash reflects that he lost the battle because he failed to plan it well, and Sanpei, coming behind him, agrees, but after noticing Ash is upset, gives him a pill made of Energy Root to recover Froakie's strength. As Sanpei turns to leave, Ash asks him to teach him the secrets of Frogadier's Quick Attack move, which Sanpei agrees to do but warns that his teachings are strict. Sanpei also adds that while he trains his Pokémon, he also trains himself. Bonnie also wants to be a ninja, so Serena outfits her, Pikachu, and Dedenne with ninja gear.
For their first lesson, Sanpei says for moves such as Quick Attack, the swift movements require muscle serving as springs. Clemont takes the opportunity to use his "Muscle Mass Magnifier Machine": shoes with springs to allow the wearer to be faster and stronger. However, the springs prove to be too strong and send Clemont blasting off into the sky. Later, Frogadier shows the group its basic exercises, and Ash encourages Froakie to give it a shot. Sanpei, wanting to combine his heart with that of his Pokémon's, begins moving back and forth, which Ash and Bonnie copy, going faster and faster. Next, Sanpei proceeds the training by learning how to run across the water's surface, which Frogadier can do easily. Froakie and even Ash attempt this feat, and Froakie after many tries is successful. Team Rocket watches from above and resolves to steal Froakie and Frogadier.
Done with the first stages of training, the group and Sanpei eat lunch. Afterwards, the group rest in the shade of a tree while staring up at the sky. Ash takes the opportunity to ask Sanpei about his hometown of Ninja Village. Sanpei says Ippei and Nihei are his two older brothers; Ippei is the best ninja in his village who uses Greninja, and Nihei is the second best, with his Venusaur. Sanpei reveals that he aspires to beat both and become the strongest from Ninja Village. Ash explains that he wants to become a Pokémon Master, with Clemont noting both are equally ambitious and are essentially rivals now.
Back at training, Sanpei aims to strengthen the power necessary for Froakie to perform Quick Attack by jumping from tree to tree, and saves Ash from falling off a cliff after a bad jump. Finally, it is time to practice Quick Attack, and the Trainer's practice by attempting to break rocks. Just then, Team Rocket comes down with a giant Meowth mech. The mech flashes blinding light and attempts to capture Froakie and Frogadier, and Frogadier sends his frubbles to block Team Rocket's viewscreen. Meowth, controlling the robot, shoots out giant gold coins, which the Pokémon evade with Quick Attack; though Froakie is hit, Frogadier hits the viewscreen of the mech, but is captured by a net. Ash commands Pikachu to use Iron Tail, but is also caught. Trying to avoid the mech's coins, Froakie ends up learning Double Team, confusing Meowth, and finishes them with Water Pulse, which Pikachu follows up with Thunderbolt. Both Froakie and Frogadier use Water Pulse to blast Team Rocket off, tearing their mecha to shreds.
Back on the road, Ash and Sanpei thank each other and promise to have a battle if they are to meet again. They bid farewell and split paths, Ash content on having expanded his Froakie's repertoire.