Feraligatr first appeared as a Totodile in Murkrow Row in Professor Elm's lab, alongside Cyndaquil and Chikorita. 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 battles against a group of Team Rocket grunts. Despite a type disadvantage, Totodile is able to defeat the grunt's Elekid, as Silver 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 meets back up with Exbo and Megaree and fought against a wild Lugia at the Whirl Islands. When Lugia attempts to crush them under its weight, Croconaw, Exbo, and Megaree work together to hold Lugia up. The strain of this causes Croconaw, Exbo, and Megaree to evolve into Feraligatr, Typhlosion, and Meganium, respectively. Though they succeed in saving their Trainers, Lugia eventually escapes.
In The Last Battle XI, Feraligatr battled 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 Team Rocket airship containing him, Silver, his loyal subordinates, and their 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. After this, he was petrified alongside his Trainer.
In The Final Battle VII, Feraligatr becomes unpetrified and regained mobility and quickly starts battling Guile Hideout's stolen Battle Tower Pokémon. Due to Silver being conscious while frozen and having 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 Dealing With A Koffing Fit, Silver arrives at Lance's secret hideout and is soon attacked by a group of Petrel's Koffing. Feraligatr fought alongside the rest of Silver's team to drive off the large horde of the Poison Gas Pokémon.
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.