Team Aqua appears in Rustboro City, where the admins (called the sub-leaders or SSS) try to kidnap the president of the Devon Corporation by capturing his Castform. When Sapphire unintentionally ruins this plan, they decide to just go through with the theft anyway, snatching some machine parts from the president and running off.
Sapphire gives chase into Petalburg Woods, where the SSS start to cream her in battle. She realizes that she is out of her depth and flees.
Later, the sub-leaders begin to enact the plan to shut Mt. Chimney down. Angie and Amber kidnap Flannery for information on Sapphire. Afterwards, Angie goes to Professor Starstone in Fallarbor Town; he has been under Team Aqua's sponsorship, and with their funding, has found a Meteorite.
Meanwhile, Amber is overseeing the operation at Mt. Chimney's summit and Ark has set a trap for Sapphire. Ark has Flannery in one of the cable cars going up Mt. Chimney, luring Sapphire in to rescue her, but he proceeds to try to drown her and Flannery by filling the car with water. However, Sapphire pokes a hole in the car to drain the water and then defeats him. She and Flannery get out of the car and onto Sapphire's Tropius.
Angie and Professor Starstone arrive at Mt. Chimney just before Ark's cable car delivers his unconscious body. Feigning panic to fool Professor Starstone, Amber explains that Ark was sent to "negotiate" with Team Aqua's enemies. He and Angie trick Starstone into thinking that Team Aqua is the good guy and they convince him to set up the Meteorite in the machine that will kill Mt. Chimney.
Amber takes off on his Pelipper to confront Sapphire and Flannery, pretending to fight badly to still fool Professor Starstone. He holds Sapphire and Flannery off long enough for Starstone to succeed in activating the machine.
Team Aqua then vanishes, victorious.
- They are rivals with Team Magma, but temporarily agree to team up in order to reach the Seafloor Cavern