Prior to A Rush of Ninja Wisdom!, Greninja was once a Froakie, as seen in a photo with Sanpei and his brothers.
Greninja debuted as a Frogadier in A Rush of Ninja Wisdom! sitting on a branch, which made Ash decide to look for its Trainer. After meeting Sanpei, Ash used his Froakie to battle Frogadier. Although Froakie tried many attacks, Frogadier proved to be too fast to keep up with. As Froakie tried Water Pulse, Frogadier disappeared in a flash. Concentrating on finding Frogadier's current location, Froakie though it had found it, only to find out it was a decoy. The real Frogadier appeared out of a nearby pond and the fight went on with both using Water Pulse. Sanpei then ordered Frogadier to use Quick Attack, which was too fast for Froakie to keep up with. Ultimately Frogadier landed the hit and Froakie was defeated.
Frogadier then aided Froakie in its training to learn Quick Attack. Frogadier showed its various techniques, such as jumping quickly from spot to spot and quickly running across the surface of the water. Eventually during the training, Team Rocket showed up in a giant ninja robot. Although Frogadier and Froakie tried to battle it, Frogadier was caught by Team Rocket together with Pikachu. Froakie now had to fight Team Rocket alone and then showed what the training had pulled off: Froakie had suddenly learned Double Team. It managed to free Frogadier and Pikachu with Water Pulse. Together with Froakie, Frogadier blasted off Team Rocket with a double Water Pulse. Afterwards it said its farewells to Froakie and the group as it and Sanpei went on their way.
Frogadier reappeared in A Stealthy Challenge!, where it was revealed to have evolved into a Greninja. Prior to the episode, Greninja battled a masked ninja's Barbaracle but it got poisoned by Barbaracle's Poison Jab and was sent flying into a river along with its Trainer. Clemont gave Greninja a Pecha Berry to cure it from the poison.
Later, Greninja battled Barbaracle again along with Ash's Pikachu and Froakie. Although Greninja and Pikachu got blinded by Barbaracle's Mud-Slap, Froakie managed to stay in the battle with Barbaracle and evolved into Frogadier, only for Saizo and Barbaracle to flee. Later, after Sanpei completed his mission, Greninja battled Ash's newly evolved Frogadier, but the outcome of this battle remains unknown.
Greninja reappeared in The Legend of the Ninja Hero!, where it walked with Sanpei, Ash, and his friends to the Ninja Village. Greninja had a battle with Nihei's Venusaur and lost.
In A Festival of Decisions!, Greninja had a battle with Heidayu's Bisharp, but was quickly defeated.
It was shown in a flashback in Facing the Needs of the Many!.