Feraligatr fist appeared as a Totodile in Murkrow Row in Professor Elm's lab, alongside Exbo and Megaree. Later, when Gold and Silver snuck into Elm's Lab, Silver stole Totodile due to a mission he received from Lance. After escaping the lab Totodile is battle against a group of Team Rocket grunts. Despite a type disadvantage, Totodile is able to defeat the grunt's Elekid, as he taught him Frustration right before the battle.
In Totodile Rock, Totodile fought against Exbo in the Sprout Tower. The two start out with Tackle and Scratch and follow up with Ember and Water Gun, giving Totodile the lead. Due to this Exbo counters with Smokescreen and gives Gold a chance to take Totodile back, but he refuses and bites him. The smoke soon sets off an alarm in the tower and activates its traps, forcing the two Pokémon to team up and stop them. In the confusion Silver escapes and Totodile evolves into Croconaw.
In Tyranitar War, Croconaw was Silver's first choice in his battle against Gold and fought against Exbo again. Croconaw starts by drenching Exbo with Water Gun and biting down on him with Bite. Exbo manages to dodge the attack with Double Team, breaking Croconaw's teeth. Croconaw recovers though and throws Exbo away.
In Lively Lugia II, Croconaw fights against a wild Lugia and meets back up with Exbo and Megaree. After a tiring battle with Lugia the three starters evolve into their final form due to the stress of the battle and the encouragement of the others. Gold then attempts to capture Lugia, but it escapes.
In The Last Battle XI, Feraligatr is used alongside Silver's other Pokémon to defeat Will by attacking with Sneasel's Beat Up. In The Last Battle XIV, he is used alongside the other starters to try and stop Pryce from capturing Celebi.
In Storming the Forretress, after Giovanni was defeated and Carr sent the flying airship containing him, Silver, his loyal subordinates and enemies crashing, Feraligatr teamed up with the other Water type Pokémon to try to keep the airship in place. However, ultimately, it was Mew who saved it from crashing. After this he was petrified alongside his Trainer.
In The Final Battle VII, Feraligatr becomes unpetrified and regained mobility. Due to Silver being conscious while frozen while he had Ultima's bracelet on he managed to pick up the skills required to teach Feraligatr Hydro Cannon, and thus was the fastest of the Pokédex holders to learn it. In The Final Battle VIII, Feraligatr, Blasty, and Mumu attack with Hydro Cannon to help destroy Guile Hideout's fake Kyogre.
In All About Arceus V, Feraligatr teams up with Exbo and Megaree to use their ultimate attacks against the incomplete forms of Dialga, Palkia, and Giratina. While the attack managed to slow them down it ended up failing.
