Omny first appeared as an Omanyte in As Gastly as Before, being sent out by Misty to try and pull down Super Nerd Miles from a sinister black fog. The dark fog reveals itself to be a Gastly and shakes him off. After the Gastly is defeated by Blue, Misty gives Omanyte to Yellow so she can better protect herself.
In The Coming of Slowpoke (Eventually), Omny used Ice Beam to seal a hole in the sinking S.S. Anne. He later used Ice Beam to freeze the legs of the Team Rocket Elite Trio, Ken, Al, and Harry and their Hypno, preventing it from attacking Yellow's team.
In Eradicate Raticate!, Omny is sent out alongside his teammates to battle against Lance and his Dragonite. Omny attacks with a powerful Water Gun, but Dragonite simply shrugs it off and throws Omny away. He is later used in a team attack to try and stop Lance from shooting bubbles. Yellow had Kitty cover the volcano crater in String Shot to form a net that is doused by Omny's water, linked to Ratty's sensitive whiskers. Upon Lance triggering the net, Ratty signals to Pika to send electricity down the net, forcing Lance's bubble into view. Yellow then orders Dody to break the bubble with Drill Peck, but the attack proves too weak.
In the final battle against Lance in The Might of... Metapod?!, after Yellow had lost the Pokédex, Omny evolves into an Omastar to gain more power. He then assisted in defeating Lance's team, attacking his Dragonite with an Ice Beam.
In Buzz Off, Butterfree!, Omny used Hydro Pump to put out a fire at the Burned Tower. In The Last Battle VII, Omny was seen defending the Day Care Center with the rest of her Pokémon from the half-masked Team Rocket Grunts.
In A Well-Journeyed Jumpluff, Omny battled Orm and his Jumpluff. Due to the spores that Jumpluff released, it made it near impossible to release a Pokémon without getting a status condition. Using her telepathic abilities Yellow moved Omny's Poké Ball outside the spores' range. Once past, Yellow released Omny and had him freeze Jumpluff with Blizzard. The attack also froze the spores as well, causing them all to fall to the ground.
When Yellow first got Omny, he was aggressive towards her, ignoring her commands and attacking her. This was due to the fact that he originally belonged to a powerful Gym Leader and Yellow had yet to prove herself to him. Over time, however, the two managed to develop a loving relationship, and now, Omny follows his Trainer's commands without hesitation. He is one of Yellow's most powerful Pokémon and is her go to pick for battling.