Ash and friends spot their ninja friend Sanpei and his Greninja floating down a river, unconscious! After they mount a rescue, Sanpei explains that he’s on a mission for his ninja master, Saizo, but a masked ninja and his Barbaracle partner keep trying to interfere.
The gang decides to help Sanpei on his mission, but soon Ash and Sanpei are separated from the others—just as the masked ninja strikes again! Froakie and Greninja team up to fight him off, and when the battle seems to be going against them, Froakie evolves into Frogadier!
The masked ninja then directs Ash and Sanpei to the manor where their friends are waiting. There, they discover their pursuer is none other than Saizo, who has been using their encounters as a test of Sanpei’s skills—and Sanpei has passed with flying colors! With everyone safely reunited, Ash challenges Sanpei to a battle, and soon our heroes are off once again to Coumarine City.
On their way to Coumarine City, Ash practices with Froakie and Pikachu. Serena, Bonnie, and Clemont continue to cheer them. During this, Dedenne and Bonnie notice something floating in the river. Ash realizes that it's Sanpei, and immediately dives to save him. Sanpei wakes up while Clemont heals Greninja of its poisoning. Everyone notices that Greninja has evolved from Frogadier since the last time they met. When they try to find out why Greninja was poisoned, they hear a voice of an enemy ninja who, along with his Barbaracle, attacked Sanpei earlier. Barbaracle attacks by using Razor Shell, but is countered by Froakie's Cut. Pikachu uses Thunderbolt on Barbaracle, who is not even affected. Team Rocket observes the situation and plans to take advantage of it by capturing Pikachu. Clemont realizes that they will be overpowered and tells them to escape so Sanpei uses his ninja power to escape from the ninja and his Barbaracle. Later, everyone is safe, but Clemont remembers that the ninja mentioned a secret document he wants to take from Sanpei. Sanpei tells them that his instructor had given him a document which was to be delivered to a Safe House before sunset; he was ambushed by the ninja soon after he left. During the ambush, Barbaracle and Greninja had a battle and Greninja got poisoned by Barbaracle's Poison Jab.
Sanpei does not know why the ninja wants the secret document, but he has to deliver it safety. They decide to help Sanpei but Clemont realizes that they have to proceed with a plan. Clemont decides to trick the ninja by inventing a device that is a mechanical body of them. Meanwhile, Team Rocket are trying to find Ash and his group. They notice footprints and hear them approaching. Jessie and James start their motto, but are interrupted by Meowth, who points out that it is a machine. An angry Jessie kicks the machine, causing it to explode. Meanwhile, Sanpei shows Ash and his friends the map and shows them where the Safe House is located. He acknowledges that they won't be able to make it during the day. He points out another route that is through the mountain but is quite dangerous. They start by taking the narrow bridge. While passing through the bridge, the bridge breaks and Clemont falls along with Serena. Clemont is saved by Froakie's frubbles while Serena is saved by Greninja's tongue.
They continue their way through a tunnel which would lead them towards the Safe House. Several Golbat start to attack them. Greninja uses Smokescreen to distract Golbat. Suddenly, Clemont falls and the Golbat use Air Slash on him but he is saved by the ninja who reveals himself as Sanpei's instructor, Saizo. Saizo takes Serena, Clemont, and Bonnie to safety. However, Ash and Sanpei escape the cave only to find that their friends got lost somewhere. Soon Saizo appears before them as the masked ninja. Sanpei tells Ash to look for Serena, Clemont, and Bonnie, but Ash insists that he will stay and battle.
Froakie and Greninja start the battle using Double Team and surround Barbaracle. Ash and Sanpei command Froakie and Greninja to use Water Pulse and Water Shuriken respectively. But Barbaracle dodges, causing Water Pulse to hit Greninja and Water Shuriken to hit Froakie. Pikachu then uses Electro Ball but is countered by Razor Shell. Suddenly, a net is thrown towards Pikachu, but he dodges. Team Rocket reveal themselves behind the net thrown. Meowth releases another net, but Saizo and his Barbaracle cut it, as Sanpei and Ash are his prey. Wobbuffet and Meowth charge to attack, but are hit by Barbaracle's Razor Shell. Using Water Pulse and Water Shuriken, Froakie and Greninja blast off Jessie, James, Meowth, and Wobbuffet for good.
Saizo, who is still not revealed to Sanpei and Ash, continues his battle, as Barbaracle uses Poison Jab, but Greninja dodges it. Froakie uses Double Team, followed with Cut, along with Pikachu's Iron Tail. Barbaracle smudges them all using Mud-Slap, negating the attacks. Barbaracle uses Poison Jab, intending on finishing Greninja. Froakie, who is beneath a rock, sees that and evolves into a Frogadier, taking the hit. Barbaracle uses Razor Shell, which Frogadier counters with Cut. Barbaracle uses Poison Jab, though gets attacked by Frogadier's Aerial Ace. Saizo uses his ninja powers and escapes, telling them they can find their friends at the Safe House. Sanpei tells that it may be a trap but they still have to continue in order to find their friends.
They come to the Safe House and are shocked to see that Serena, Clemont, and Bonnie are safe. Saizo again reappears although masked. He removes his mask and Sanpei recognizes him as his master. Saizo tells him that he was the one who took Serena, Clemont, and Bonnie because he did not want to involve Sanpei's friends in this. Saizo also wanted to drag Ash out of it but Ash and Sanpei were out of the tunnel. Serena then sees that Ash's Froakie has evolved into a Frogadier. Bonnie tells Frogadier to return back to a Froakie and then evolve in front of her as she wanted to witness its evolution. Seeing the opportunity, Ash along with Frogadier challenge Sanpei and Greninja. The episode ends with Sanpei and Ash battling although the outcome is unknown, as the journey continues.