Prior to Sanpei's journey as a ninja, Sanpei got Greninja as a Froakie from his brothers.
Sanpei's Greninja first appeared as a Frogadier on the tree along with his trainer. When Ash challenged Sanpei to the battle, Sanpei decided to choose Frogadier as Ash's Froakie's opponent. Frogadier using its speed and attack dodged many of Froakie's attack. On its turn, it managed to defeated Froakie with only a few hits. Later it helped Froakie to try and learn Quick Attack, but Froakie ended up learning Double Team instead. He also defeated Team Rocket in the process.
Sometime later, Frogadier evolved into Greninja. During its training, Sanpei and Greninja were confronted by a mysterious masked man and his Barbaracle. Greninja battled the masked ninja, but ended up getting poisoned by Poison Jab and both Greninja and its trainer were sent flying into a river. Luckily, Sanpei and Greninja were rescued by Ash and his friends. Soon, Greninja battled alongside with Ash's Pikachu and Ash's Froakie against Barbaracle. During the battle, Greninja and Pikachu got blinded by Mud-Slap and just when they were about to be defeated, Froakie jumped in between and protected them from the attack, evolving into Frogadier in the process. Frogadier defeated Barbaracle with his newly learned Aerial Ace, but Barbaracle and its trainer retreated. Afterwards, Ash and Sanpei learned that the masked figure was none other than Saizo, who appears to be Sanpei's mentor. Saizo explained that the entire incident was only to test Sanpei's skills he learned from his journey. Once Sanpei got his scroll and completed his mission, Sanpei and Ash decide to battle each other while the outcome of the battle is unknown.
During the assault on the village, Greninja once again battled alongside with Ash's Pikachu and Ash's Frogadier. But this, it battled against Heidayu's Bisharp. However, Greninja was immediately defeated until Saizo and his Barbaracle arrived to save them. After coming up with a plan to rescue Hanzo from Kagetomo, Greninja, Pikachu, and Frogadier battled Heidayu's Bisharp to provide a diversion for Ippei and his Greninja. During the battle, Greninja and Pikachu were defeated, but Ash's Frogadier protected them from Bisharp's upcoming attack, evolving into Greninja in the process. Ash and Greninja both synchronized their feelings and used a special form to defeat Heidayu and his Bisharp.
Greninja was later seen in a flashback before Ash released his Greninja.