The episode begins in the darkness of the night in the middle of a forest. Everything is silent, apart from one ear-piercing sound coming from one, lonely crying Bonsly. The next day, we find Ash, May, Max and Brock enjoying a spot of lunch while relaxing as a group around a tree stump. Ash, Max and Brock are enjoying some tea, as May looks happily at her egg while polishing it with a cloth. May can't wait for the egg to hatch, and Max wonders what Pokemon could possibly be ready to come out of it. Maybe a Water or Grass type, he ponders. May hugs her egg and says that she isn't bothered what hatches, but she has a good feeling about it. Ash gets up, and suggests to Pikachu that they try out some Volt Tackle training. Pikachu agrees, and soon after the group are prepared to watch a training session consisting of Ash, Pikachu and Donphan.

Ash orders Pikachu to use Volt Tackle, and Pikachu does so, speeding towards Donphan while huge levels of electricity are generated around its body. Donphan stomps the ground and gets its footing to prepare itself for the heavy blow, before Pikachu slams into it with the full power of Volt Tackle. Donphan stands strong, keeping its footing and doing its best to resist the sheer force of Pikachu's power. Just as it looks like Pikachu is going to gain the upperhand, Donphan focuses and throws Pikachu back. Pikachu is thrown, but lands perfectly on its feet as Ash thanks Donphan for its help and compliments it on its ability to deflect the blow. May, Max and Brock sit amazed at the shows of power on display. Just as Ash is about to get Donphan to perform an attack of its own to see how Pikachu holds up, Donphan suddenly rolls up into a ball and uses Rollout to rip straight through Ash and Pikachu and smashing into a rock. Ash and Pikachu are sent flying back, but just as Ash is about to ask Donphan what's up, e notices the reason: A lone male ninja, along with a Ninjask, was hiding behind the rock, and Donphan believed him to be a threat.

Sometime later, we find the ninja, sitting on the tree stump drinking tea surrounded by the group. The boy is impressed to hear that Ash in on the Battle Frontier challenge, but Ash stops him and asks him why he was watching them. The boy bows and apologises, and Ash says that it's alright, but doesn't press the matter further. He then introduces himself, and Max, May and Brock do the same. The boy then says that his name is Koroku, and that he's a student in the Pokemon Ninja School. Ash repeats the words, and Koroku explains that the school trains you and your Pokemon with the ways and abilities of the ninja. Koroku then offers to take them to the school, and the group agree.

Sometime later, the group have reached the school and have changed into their ninja clothes in order to train there. The leader of the school is briefing them and the other members of the class of sorts, which consists Koroku, a girl with a Tangela, a boy with a Bellsproat and another boy with an Ariados. Several of the students speak up, and tell their teacher about several strange things that have been happening around the school as of late... gates being left open, and weird wailing sounds coming out of the forest. The leader, Ichigo, tells the group that they'll have to investigate this as a matter of the security, and the group agree. Brock even more so than the other however, as he proclaims his undying love and dedication to Ichigo. Brock then lunges at her, and hugs Ichigo tight... before realising that he's actually hugging a log wearing a ninja shirt. Brock steps back thinking that Ichigo has been turned to wood, before the real Ichigo calls down from above them, telling them that such such evasiv tactics are necessary for a ninja to learn.

Watching all of this is Team Rocket from a group of bushes just outside of the school. Jessie suggests that they should try to nab Pikachu and all the other Pokemon in the ninja school, but James isn't sure. Shouldn't Pokemon that have been trained in a ninja school be really hard to steal? Jessie doesn't seem to be listening however, and goes onto to tell them her dream of being a Beautiful Ninja. James and Meowth repeat her words in disbelief, and then sigh. Jessie then goes onto describe her childhood dreams of being a Beautiful Ninja... running at the speed of light through a dark forest at night, before jumping out at her enemies and throwing a Starmie at them as it uses Water Gun to defeat them and send them flying out from their hiding places. James, Meowth and Mime.Jr. aren't listening however, as they continue to watch Ash and co. inside the ninja school. Seeing this, Jessie screams at them to pay attention.

Elsewhere, Ichigo is training the group on breathing underwater using bamboo shoots to be able to hide and breath beneath the surface. May and Max soon give in and burst up to catch some real fresh air. Soon after, the other students and their Pokemon come to the surface in order to breath. Ichigo then tells them that the next lesson will be hiding using your surroundings, and blending into the area. A little later, a group of three Pidgey fly down to enjoy some food and to rest. They look around to see if anybody is about, not seeing Max hiding beneath a fake layer of bark on a tree, or noticing that the ground beneath them is fake and contains a very annoyed Ash. The force of the Pidgey walking all over him gets too much, and he bursts out of the ground and scares the Pidgey off. Ichigo then emerges from beneath another layer of fake bark that she was using to conceal herself like Max, and tells that it's okay: It takes some time to get used to handling such conditions.

The students are then brought together, and Ichigo explains their next task. She calls out another of her Pokemon, Kecleon and tells her students that Kecleon will be using its special ability to turn half-invisible, and that their jobs will be to find it. Kecleon then shoots out into the forest, and the students follow. Ash and Koroku go off as a duo to try to find Kecleon. Ash is having some trouble spotting it, so Koroku tries to focus his ninja senses to try to locate the Pokemon. Soon enough, he senses something and then orders Ninjask to use its wings to create a storm of dirt. Ninjask does so, and the dirt cloud settles on Kecleon and reveals itself. Koroku jumps at Kecleon, and is surprised when he lands on nothing but air as the tail of Kecleon covered in dirt vanishes. Looking up, he sees Ichigo coming towards him saying that he did good in sensing her Pokemon. Koroku smiles happily and thanks her for her compliment, and Ichigo lets Ash have a go at sensing Kecleon. After some time, Ash orders Pikchu to attack a nearby group of bushes, believing Kecleon to be there. However, as Pikachu performs the attack, Ash's hat comes off his head and flies all the way up a tree... when it reaches the top, Kecleon reveals itself, having been hiding on Ash's head without him noticing. Ash jumps at the crafty Pokemon, but Kecleon dodges and Ash smashes straight into the tree.

Elsewhere, the other group of students, along with their Pokemon, are looking around for Kecleon also. One of the male students hears a sound coming from the long grass. Going over to look, he pulls aside the grass to find a small wandering Bonsly. Bonsly tries to run away, but the ninja student grabs it quickly and turns around to show his team mates. The Bonsly then begins to cry extremely loudly, and the group wonder what they've done to make it so upset. At that, Brock then appears and tells the boy that he's handling Bonsly all wrong... it is young, after all. Brock then cradles Bonsly in his arms and rocks it back and forth while telling it that everything is okay and that they won't harm it. Bonsly then calms down, just as Ichigo, Koroku and the rest of the students appear on the scene. The group is surprised to see Bonsly in Brock's arms, and Ash checks the Pokemon on his Pokedex. The three students that found the Bonsly shout at Brock, saying that Bonsly is probably the Pokemon that has been causin so much mysterious things to happen around the school as of late.

Brock tells the three to calm down, and to let him handle Bonsly. He pulls a dark blue berry from a nearby bush, and puts it to Bonsly's mouth. The Pokemon doesn't seem too impressed at the food, and bats it away with its head. Brock smiles at this however, and then prepares something he says he thinks Bonsly will like: A baby bottle. Bonsly happily sucks on the bottle until all the milk in gone. Once the milk runs out, Bonsly begins to cry again before smacking Brock in the head with its own head, and then keeps on attacking Brock to push him away. At that moment, Ichigo senses something and tells the group to watch out as a ninja star is thrown at them, before hitting the ground and opening up to reveal a single red rose. The group look at the rose in amazement, wondering what in the world is going on, before Jessie calls out to them and begins the Team Rocket motto. After the motto is finished, the group look up at Team Rocket, who are drssed as ninjas and tied to a large paper kite mecha with huge robotic arms. Kokoru asks who Team Rocket is, and Max explains that they're a group of villains that are always trying to steal Pokemon.

Jessie starts things off by ordering Meowth to let off one of the mecha's attacks, which consists of a large amount of sticky thread which grabs all of the group's Pokemon. Ichigo isn't about to let Team Rocket get away however, and sends out her Shiftry before ordering it to chase after the villains. Shiftry does so, speeding after Team Rocket's kite and cutting the string which keeps it afloat. Team Rocket then fall to the ground, and Shiftry lands perfectly. Ash, May and Brock then send out Grovyle, Combusken and Marshtomp to join Shiftry and to help it get back all their Pokemon which are hanging along with Team Rocket on a nearby tree. Ash orders Grovyle to use Leaf Blade to cut the sticky string holding the Pokemon, releasing them all. May follows up by ordering Combusken to use Fire Spin, which burns Team Rocket and their kite. The villains are then sent falling from the tree by Marshtomp, who uses Water Gun.

Watching all of this is Bonsly, who is amazed at the group's power and friendship. Jessie shuts at the group, saying that they can't stop a Beautiful Ninja like herself. Ash and Brock stare in disbelief at Jessie, who sends out Seviper to use Smog to hide her, James and Meowth. Jessie then jumps up into the air with a huge net, and uses it to capture Ichigo. The smoke clears, and Jessie laughs at her capture. However, Ichigo appears behind her laughs, which causes Jessie to stare in shock... she's supposed to be in her net! Jessie lifts the net up, to reveal, just like Brock found, a log in Ichigo's shirt. Jessie turns and says that she isn't beaten yet, as she performs a Double Team attack of her own... she seems to consist of running around, with James and Meowth dressed up as Jessie to create the illusion of their being several images of her.

Ichigo isn't impressed, and orders Shiftry to use Double Team to stop all the nonsense. Shiftry does so, using the clones of itself to stop Jessie, James and Meowth in their tracks. She then orders her Pokemon to use Razor Wind, which is followed by Korokuwho orders Ninjask to use Fury Swipes, and Ariados to trap Team Rocket in a ball of String Shot. Brock scolds Team Rocket for their actions, and the group let slip that it was them that have been skulking around the ninja school as of late. The students aren't impressed, but before they can do anything, Team Rocket roll off, still trapped in a ball of string shot. Ash is about to go after them, but Ichigo stops him and says that they'll find themselves in trouble soon enough. Which they do, as they roll off the edge of a cliff, get caught on a branch, and the force of hitting the branch sends them bouncing right back into the air and blasting off again.

Ichigo thanks Ash and co. for their help dealing with Team Rocket, and Brock becomes over-excited at her praise. Just as he is about to go hug her again, Bonsly appears and smacks him in the head again. Brock is sent flying to the ground, but gets up when Bonsly begins to cry again. The three students start to scold Bonsly, but Ichigo stops it and says that she understands... it's been all alone and afraid for so long. Bonsly is about to start crying again, but Brock starts talking to it, and manages to get the upset Pokemon to calm down. Brock asks if it would like to come along them then, and Bonsly smiles and nods, but then suddenly jumps into Brock's arms again and starts to squirm. The group wonder what possibly could be up with Bonsly, before Ash realises that Bonsly wants a battle with Brock... sort of a way to prove itself. The battle begins, and Brock calls upon Forretress as his battling Pokemon of choice. Just as Brock is about to order an attack, Bonsly starts to cry again which puts Brock off-gard as he wonders whether a battle really is a good idea.

However, the tears turn out to be one of Bonsly's moves, Fake Tears, and Bonsly takes this moment to attack Forretress and sent it flying back into a tree. Brock nods and understands, and tells his Pokemon to use Rapid Spin. Forretress does so, and Bonsly starts to cry again. Brock tells Forretress to ignore it however, and Rapid Spin smashes straight into Bonsly and sends it flying back. As Bonsly lands, Brock calls for a Spikes attack which surrounds Bonsly which several sharp spikes. Seeing that Bonsly is unable to escape, Brock throws a Pokeball, which sucks Bonsly inside of it. However, Bonsly soon breaks out, only to land on the floor again, topple over and be hurt by one of the Spikes laid down before. Brock then throws out another Pokeball, and this time it works after Bonsly had suffered some damage. The group congratulate Brock on his capture, as Brock celebrates by holding the Pokeball in the air, ala Ash.

Sometime later, Bonsly is out and crying once again, before Brock uses a bottle to calm it down. Ichigo says that Brock was really cool when he captured Bonsly, but then deflates his ego by saying he makes a really good father. The group laughs, and Ash and co. part from the Ninja School after saying their goodbyes.

The episode ends with the group walking off into the sunset, with Brock still taking care of his brand new Pokemon.

Thanks to Alfonso for writing this for us