During a night, a Pokemon, left abandoned, cries. Next day, the gang has lunch. May expects the egg to hatch soon. They do not know which Pokemon it will be, making it exciting. Ash goes to practice Pikachu's Volt Tackle. He sent Donphan - Pikachu charges with Volt Tackle, though Donphan brushes him off. Ash orders to do it once more, but Donphan, for some reason, beings to roll, so they all get away from its path. Donphan crushes a rock and a ninja and his Ninjask were hiding. The ninja thought they were thieves, but was explained they were crossing the Battle Frontier. The gang introduces themselves and the ninja is Evian, the student of the Ninja school.
The school teaches the people and Pokemon the arts of the ninja. They decide to go there and enlist. The teacher tells there have been reports of thefts - the students confirm this and one saw a shadow running in the bushes yesterday and he also heard the cry. Brock flirts with the teacher and hugs her, but he hugged a log - the teacher swapped using the ninja skills. Team Rocket see them all and Jessie recalls her days as a ninja. Later, the students are in the lake, breathing through some pipes. They suddenly come out, as the lesson was to become one with the lake. Later, they all are disguised. The Pidgey peck the ground, so Ash and Pikachu come out, as they couldn't handle the pain. So, the teacher decides to practice endurance.
The teacher sends Kecleon. She tells Kecleon is going to disappear, so they need to find it. Kecleon disappears, so everyone goes to search for it. Ash and Pikachu search, but cannot find it. A student tells that he needs to use the ninja skills to detect it. He senses something, so Ninjask sprays the dust - the tail is seen. He goes for it, but almost captures it, as Kecleon disappeared very quickly. Ash tries the same - Pikachu uses Thunderbolt, but during the attack, Kecleon snatches Ash's hat. They go for it, but it gets up, so they fail. Other students go to search and one finds a Pokemon and grabs it. The Pokemon cries, so other students recognizes it is the same cry he heard yesterday. Brock gets the Pokemon and calms it - it is a Bonsly.
The students demand their stuff back, so Brock tells asks them why proof they have Bonsly stole the stuff. One answers he heard the cry, so Brock reaches for a berry and offers it to Bonsly. Bonsly cannot reach the berry, so it pounds it. So, Brock gives Bonsly some milk instead, so Bonsly drinks it. Nevertheless, Bonsly cries and pounds Brock. Suddenly, Bonsly senses it is attacked and evades a shuriken. It is Team Rocket - they release the strings to get the Pokemon and go away. The teacher sends Shiftry - Shiftry cuts the kite they have been attached to, so they fall down on a tree. Ash sends Grovyle, May Combusken and Brock Marshtomp.
Grovyle cuts the strings with Leaf Blade, setting the Pokemon free. Shiftry uses Rock Smash, hitting Team Rocket. Combusken burns them using Fire Spin and Marshtomp makes them fall to the ground with Water Gun. Jessie tells she has ninja skills and challenges the teacher. Jessie sends Seviper, who uses Haze. Jessie grabs the teacher with a net, but the teacher appears behind her - she used the same trick before, so Jessie caught a log. So, Jessie "uses" Double Team (so James and Meowth run with her dressed the same way as her). So, Shiftry uses (properly) Double Team. Next, Shifty uses Razor Wind and Ninjask Fury Swipes, scratching them. Ariados uses Spider Web, immobilising them. Brock asks them if they stole some berries, to which they confirm.
The students now know they stole the berries, so Team Rocket rolls away. However, they bounce off a tree and blast off. Angela (the teacher) thanks Ash, but he does not want any credit, so Brock flirts and tells she is the one who saved. Suddenly, the Bonsly tackles Brock. Bonsly cries, so they suspect it thanks Brock for standing in its defense. The students condemn it for running away from Team Rocket, but Angela tells them Bonsly is weak and young. Brock tells it is alone, but offers it to come with him. Bonsly is happy, but suddenly feels upset and goes after Brock. Ash realizes Bonsly wants to battle Brock, to prove its strength.
Brock accepts the battle and sends Forretress. Bonsly cries, letting Brock off his guard and attacks Forretress. Forretress uses Rapid Spin and ignores Bonsly's tears, knocking it out. Next, Forretess produces Spikes, so Bonsly does not spin anymore. Brock sends the Poke Ball, but Bonsly frees itself. Bonsly is happy, but accidently gets on one of the spikes, so Brock sends another Poke Ball, but this time he captures it. Later, Bonsly cries, so Brock gives it milk to calm down. Still, it throws the bottle to Brock, so Brock yells milk is all what it'll get, so stops crying. Angela tells Brock's a dad now, taking care of Bonsly. Later, the gang goes away.