After Team Aqua successfully flooded the Hoenn Region with Kyogre's power, they went to the next closest region: Kamla. Once there, they were defeated by a protagonist clad in Blue, and most team members went into hiding or were arrested, including the leader Archie.

Two and a half years later, the team is reformed into the Blue Ribbon under Matt and Shelly. Interested in revenge for their loss, they begin the ultimate plan to create Genesect. This is when Alchemist takes place.

The player, on a journey through the Kamla Region, meets characters like Looker and Colress, who want to stop the Blue Ribbon. The Blue Ribbon is stopped in Graphite City, Sandveil, and Icepick before they are finally defeated in the final culmination of action at their base. Genesect is defeated and most team members are once more arrested, Matt and Shelly included.

In the postgame, remaining members reform under Allen: an angry Grunt who won't accept defeat. Wreaking havoc in North Kamla, they are defeated by the Player and the Champion.