Team Aqua

Though they are first encountered early in the game, their first major plot is to use the Meteorite to cease the eruption of Mt. Chimney, which would cause rainwater to fill the cooled-down crater. When this is thwarted by the player, they set themselves up in Lilycove City's cove, planning their next moves. Their final action in the storyline is to steal a submarine from Slateport harbor, which they use to travel to the Seafloor Cavern with the Red Orb, where Kyogre awaits. Kyogre, however, is not able to be controlled, and leaves for the Cave of Origin in Sootopolis City where it must be captured by the player or defeated.

Team Aqua is relegated to a supporting role in Ruby, with Team Magma instead performing the same actions (with different reasoning) and awakening Groudon instead.

Team Aqua's deeds are partly the same in Pokémon Emerald as they are in Sapphire, with them stealing the sub to obtain Kyogre. After awakening Kyogre and seeing Kyogre and Groudon clash together, both Team Magma's Maxie and Team Aqua's Archie realize what they've done has caused a terrible disaster, and make peace with one another after Groudon and Kyogre have been taken care of by Rayquaza.

In Pokémon Alpha Sapphire, Team Aqua's role in the story remains largely the same but their motivation has been significantly altered. While in the original versions of Ruby and Sapphire Team Aqua saw a world with more seas as ideal for both Pokémon and humans, in Alpha Sapphire Team Aqua wishes to expand the sea to wipe out human civilization and return the world to its beginnings, so that Pokémon can live untainted by humanity's progress. This puts them in direct opposition to Team Magma, who in this version of the story believe that the land must be expanded to progress human living conditions.

Team Aqua in the anime

Team Aqua was introduced in Stairway to Devon where a member of the team infiltrated the Devon Corporation and stole two capsules of "Creation Fluid". His plans were stopped by Team Rocket's Jessie and James, who intended to steal the same thing, all parties involved not realizing that "Creation Fluid" was nothing more than water. In On a Wingull and a Prayer!, this same member took a boat of Mr. Briney's to escape from the police and headed for open ocean, where a Team Aqua submarine rescued him. This particular grunt is voiced by Darren Dunstan in English.

Team Aqua later appeared in A Three Team Scheme and Unfair Weather Friends. Their final, and most prominent appearance was in Gaining Groudon and The Scuffle of Legends, when they and Team Magma began the battle between Kyogre and Groudon.

Team Aqua in Pokémon Generations

Team Aqua appeared in The Cavern, where Archie and three Grunts explored the Seafloor Cavern in search of Kyogre. Upon finding Kyogre, the Aqua Leader used the Blue Orb to awaken Kyogre's Primal form, despite Shelly's protests. Their scheme didn't go as planned, however, and the team was forced to watch as Kyogre devastated the Hoenn region. Aboard the Submarine Explorer 1, Archie and Shelly were last seen getting attacked by Primal Kyogre.

Team Aqua were portrayed as more influential than their counterparts Team Magma. Their leader Archie, as the director of Hoenn TV, was able to orchestrate a cover-up of Team Aqua schemes and the identity of the team itself, while reporting Team Magma schemes and airing anti-Team Magma propaganda whenever they could. This was how Gabby and Ty seemed to be unable to tell the full story of what happened to Mr. Stone on Route 104, or the ending of volcanic activity on Mt. Chimney, a successful scheme led by the Aqua Admins. In addition, Team Aqua's headquarters in Lilycove City was able to house countless aquariums of Water-type Pokémon.

Team Aqua's influence on the media eventually became too much for one man - Magma Leader Maxie, who went to Lilycove to confront Archie. Archie eventually settled on a truce with Maxie which involved the two teams combining forces to reach the same destination together, as while Team Magma held the submarine built by Captain Stern, Team Aqua had control of the Devon Parts they stole from Mr. Stone, which enabled the submarine to reach its destination.

The ending of volcanic activity was expected to bring the conditions necessary for Kyogre to quickly gain areas of influence once it awakened. However, this was not the case, and Archie sent Amber over to investigate. Once Archie obtained the Blue Orb, he trapped Amber in the submarine they took to get to the Seafloor Cavern, as well as the Blue Orb's previous holder Tabitha. Moreover, Archie took out the Devon Parts from the submarine and put it on auto-pilot so that it would burst. Despite surviving this event, Amber swore his allegiance to Team Aqua and joined forces with his fellow Admins to confront the Hoenn Gym Leaders who were also impeding Kyogre's advance.

Archie disbanded Team Aqua shortly after assuming his new guise.

Archie returned at the same time that Neo Team Aqua (Japanese: 新生アクア団 Neo Aqua Gang) were formed by new incarnations of Matt and Shelly, to cooperate with Zinnia.