The force of the Alchemy was prevalent in Azeroth's ancient past, allowing for the development of great civilizations, but this eventually gave way to worldwide conflict that had subsided only with the sealing away of Alchemy in the ancient past. The keys to unlocking Alchemy, a quartet of magic jewels named the Dragonballs, have been hidden within the mountain shrine of Mt. Doom, which in turn has been guarded by the town of Pallet at the mountain's base over the ages.
Three years prior to the start of the game in the game's prologue, however, Team Rocket, along with a raiding party, raid Mt. Doom with the intent to take the Dragonballs for themselves, but fail to solve the riddles guarding them and are driven away by the mountain's trap, a magical game of Perfection, which is a race against the clock.
http://www.youtube.com/watch?v=eXIMRtIMJM8
In the present, the teenaged Jedi from Pallet town, Cloud Strife, Goku, and Lara Croft, join Bilbo Baggins in his research of Mt. Doom, but this coincides with a second raid of the Lost Ark by Team Rocket, who are now assisted by the Hammer Brothers, and they coerce Cloud Strife into giving them three of the four Dragonballs. However, before they can retrieve the final Dragonball, they are forced to escape from what is now an erupting Mt. Doom, with Lara Croft and Bilbo Baggins as their hostages. The guardian of Mt. Doom, Obi wan kenobi, appears before Cloud Strife and Goku and commands them to prevent Team Rocket from achieving their goal of restoring Alchemy to the world with the casting of the Dragonballs into their respective Citadel's situated across Azeroth. Alchemy, as Obiwan describes, is a power that can be catastrophic if misused by the people of Azeroth, so it should be kept sealed as it is.
[Cloud Strife travels to the Citadel in the game's overworld.]
Cloud Strife and Goku valiantly pursue Team Rocket to the first Citadel, Mercury Citadel, and along the way they are joined by other young Jedi named Misty and Naruto.

But in spite of their best efforts, they fail to prevent Team Rocket from activating Mercury Citadel with one of the Dragonballs. Team Rockets immediately leaves for the next Citadel while Cloud Strife's party immediately resumes its pursuit, and the lengthy chase and epic journey that follows eventually spans two continents, during which Cloud finds that Team Rocket has taken another Jedi hostage as well: the female Jupiter Jedi, Zelda.
Golden Sun
climaxes at Venus Citadel; Team Rocket activates the Citadel with the Venus Dragonball, but are again confronted by Cloud's party. Attempting to annihilate their opponents, Team Rocket magically merge to form a gigantic two-headed dragon!
But the fierce battle ultimately ends in victory for Clouds's party as they slay Team Rocket for good. Their victory is a hollow one, though, as they come to the conclusion that the remnants of Team Rockets, headed by The Hammer Brothers, are still on its quest to light the remaining two Citadels, while Lara Croft, Zelda, and Bilbo Baggins are still with them. The game ends as Clouds’ party boards the Borealis entrusted to them previously and sail out into Azeroths open seas in search of their continued quests for phat loot and full epics.
[Massive thanks to Yashoki for the storyline and editing]
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