Gomamon is a Vaccine-type Rookie Level Digimon of the Deep Savers family. He first appeared in the Digimon Pendulum Version 2.0.
When Gomamon first meets Joe, he is not Gomamon at all, but is instead in his In-Training form of Pukamon, as is the case with all of the other partner Digimon. Joe is initially quite freaked-out by Pukamon's appearance, but this does seem to bother Pukamon any. Pukamon evolves to Gomamon when the group is attacked by Kuwagamon. He is the only Digimon not to use his special technique in the battle, instead opting to help out by rolling under one of Kuwagamon's feet, tripping the Insect Digimon. When the group falls off a cliff as a result of this first battle, Gomamon is able to save them by using his special technique, Marching Fishes. Marching Fishes allows Gomamon to call in multicolored fish to assist him in battle. In this case, the Marching Fishes are able to form a raft that carries the team to safety.
Gomamon does not see any more major action until the group gets into an argument regarding whether or not they should take the risk of scaling Infinity Mountain to get a good fix on the layout of File Island. In an attempt to placate everyone, Joe sneaks away while the others are sleeping, seeking to take on all the risk by himself and keep everyone else safe. Gomamon accompanies him on his quest, and along the way, they are attacked by Unimon, a flying unicorn Digimon who is possessed by a Black Gear. By this time, Tai and Greymon and Sora and Birdramon have attempted to come to Joe's rescue, but Birdramon and Greymon cannot stand against Unimon. When Joe flings himself at Unimon in an attempt to pry the Black Gear free from the Digimon's back, he puts himself in enough danger that Gomamon is able to evolve to his Champion form of Ikkakumon, with the special technique of Harpoon Torpedo. Ikkakumon is then able to defeat Unimon and free him of the Black Gear. From this point on, Gomamon is able to evolve to Ikkakumon in times of crisis.
The Dark Horse Digimon series only covers the first arc of the animated series. It does not get to the point at which Gomamon evolves to his Ultimate form of Zudomon, which is during a battle with MegaSeadramon in the real world during the Myotismon arc.