James's Amoonguss first appeared in New Places... Familiar Faces!, debuting along with Jessie's Frillish when Team Rocket attacked Ash and his friends for the first time since their "Operation Tempest" and temporary retreat back to Kanto.
When Ash and friends were helping the rookie Trainer Nanette to gain some experience, Team Rocket surprised them, sent out their new Pokémon, and used a combination of Mist and Stun Spore on them and their Pokémon, reducing the visibility to almost nothing and paralyzing Iris's Emolga and Cilan's Stunfisk at the same time, thus leaving Ash alone to face Team Rocket with Pikachu. Using the Mist as his advantage, James had Amoonguss use Body Slam, which was strong enough to actually knock Pikachu out. As Ash sent out his Unfezant to blow the Mist away, Team Rocket was close to stealing Pikachu inside of their mecha. However, thanks to the distraction of Nanette and her Tepig, Pikachu was freed, although Tepig got caught in the process. For a getaway distraction, Team Rocket fired a combination attack of BubbleBeam and Hidden Power, which, much to their surprise, was endured by Unfezant, followed by an Air Cutter and an Aerial Ace to defeat Frillish and Amoonguss, respectively.
Amoonguss reappeared in The Name's N!, where James sent it out after catching Pikachu. It distracted Ash from holding on to his Snivy when she used Vine Whip to grab onto their balloon. It once again battled Unfezant after Axew freed Pikachu with Dragon Rage. Pikachu joined in the battle and tried to finish off Team Rocket but Amoonguss paralyzed him with Stun Spore before the attack completely blasted them off. Amoonguss was taken out along with Frillish by Unfezant's Air Cutter which slammed them into Team Rocket's balloon.
Amoonguss was used to battle Aldith's Liepard in Team Plasma's Pokémon Manipulation!, alongside Woobat as Jessie, James and Meowth tried to steal Colress's Pokémon manipulation machine. Eventually Liepard's Shadow Ball veered and hit Colress's machine, releasing Iris's Dragonite and Rhoder's Haxorus which were under his control.
After Team Plasma took control of Meowth with their machine in Meowth, Colress and Team Rivalry!, Jessie and James decided to attack their friend in order to get him out of the trance. James commanded Amoonguss to use Stun Spore and paralyzed Meowth, then use Body Slam so they could completely weaken him, orders that it didn't hesitate to fulfill. Having Meowth out of Team Plasma's control, Team Rocket managed to get out of their headquarters using Frillish's Mist.
Amoonguss was given away to Giovanni for Team Rocket in The Dream Continues!.