As the first Pokémon sent out in their battle. Nidoqueen used Counter against Red's Snor, which blasted it into the wall of the gym. He then switched it for his Golem. As Red was on the floor, Giovanni was, in a sense, looming over him with his Pokémon, including Nidoqueen. As they were on their last Pokémon, they put them back in their Poké Balls to send them back out again in order to see who can defeat the other in the quickest time. He sent it out, but before he could command an attack, Pika used Thunderbolt on them, which also knocked out Nidoqueen, despite the type matchup, to which Red explained that he was wearing Team Rocket gloves that prevent the user from being electrocuted, meaning Pika could charge itself up inside its Poké Ball. Yellow explained to Red after his battle with Giovanni and his Pokémon, the former had collected Red's blood from the battlefield.
To pop the bubbles created by Lance that caused pain when they hit someone, Giovanni sent out Nidoqueen to pop them with Scratch. While trying to pop the main bubble that was creating them, Lance had his Dragonair use Hyper Beam, which knocked out Nidoqueen.
Along with Nidoking, Nidoqueen defended Giovanni from a bike gang.