When the Aqua agent was cornered by the heroes and Mr. Stone, he sent Crawdaunt. Crawdaunt got hit by Pikachu's Quick Attack and retaliated with Crabhammer, then used Bubble Beam to attack everyone. This allowed the Aqua Agent to use his jetpack and fly off as he called Crawdaunt back in its Poké Ball.
The next day, the agent had to find means to contact his fellows at the submarine. He sent Crawdaunt to intimidate Peeko and threatened to hurt it if Mr. Briney would not accomplish his tasks. When the Aqua agent was to sail off, he heard the heroes coming and sent Crawdaunt to battle them. Team Rocket appeared and sucked away Peeko and Pikachu, so Crawdaunt blasted them off with Bubble Beam. Crawdaunt took Peeko and sailed off with the Aqua agent, towards a point, where they'd meet up with their associates. Seeing the heroes and Mr. Briney following him in a ship, Crawdaunt launched Water Pulse and Bubble Beam, nearly hitting the ship. Though the Aqua agent dropped Peeko's cage, he and Crawdaunt managed to come to Team Aqua's submarine and have fled.