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The story begins with a cut-scene where the {{player}} is to have been unconscious on a beach due to a time-traveling accident, causing him/her to become a Pokémon. Meanwhile, the partner is nervous about joining the [[Wigglytuff's Guild]], a local exploration club, and gives up early. Walking along the beach, the partner encounters the player, and informs that the player has been turned into a Pokémon. The [[Relic Fragment]] the partner holds is then stolen by {{p|Zubat}} and {{p|Koffing}}, members of [[Team Skull]], which the player helps recover. After a brief exchange, the partner explains their motivation for joining the guild. The player's partner loves legend and lore and their life dream is to find the secret of their personal treasure-a Relic Fragment with a strange pattern on it. The partner, reinvigorated by the player's courage, joins the Guild as a new team with the player.
Over the next few days, the team gets accustomed to life at the Guild and the nearby [[Treasure Town]]. Among the folks they meet are {{mdc|Wigglytuff|2}}, the kindhearted Guild Leader, {{mdc|Chatot|2}}, the hot-tempered yet well-meaning second-in-command, {{pmdc|Bidoof|2}}, the newest recruit prior to the team joining, the Guild chef {{p|Chimecho}} (also in charge of maintaining the team), {{p|Diglett}} and {{mdc|Loudred|2}}, the Guild sentries, {{p|Dugtrio}}, maintainers of the job boards, {{p|Magnezone}}, the local sheriff, and other exploration teams. As they are introduced to the Guild, they learn of the fact that rogue Pokémon have been wreaking havoc in the world due to the disruption of time, Pokémon cannot [[evolution|evolve]], and new "Mystery Dungeons" have been revealed and open to exploration.
The player discovers not too long after that he/she has the ability to spontaneously see things in the past and future, but only when touching an object of some kind. This is known as the [[Dimensional Scream]], as revealed later by {{pmdc|Dusknoir|2}}.
===The legend of the Time Gears===
===Escape from the future===
The player is woken up by the partner, who reveals that they have been locked in a cell. Just then, they encounter some guards—a group of {{p|Sableye}}. Six Sableye blindfold them and take them to another room, where they find themselves bound to a pole, awaiting execution. Along with the two is Grovyle, also tied up. Dusknoir appears, giving the orders to the Sableye to execute the three. Grovyle convinces the team to cooperate - while the Sableye to attack the ropes that tie them to the stake, there is a slight chance of breaking the ropes, and it may allow the three to escape. Fortunately, the ropes break free, and the three overwhelm the Sableye. This allows Grovyle to use a [[{{DL|Wonder Orb|Luminous Orb]]}}, and take the team to safety. Back outside, Grovyle reveals that they are indeed in the future, but despite the lake trio returning the Time Gears back to their original places, the planet has been paralyzed.
Continuing to elude the Sableye, the partner loses confidence on whether they will ever return home. The player then proposes to the partner to catch up to the Grovyle, and ask how he had traveled back to the past in the first place. They eventually catch up to Grovyle, and save him from the {{p|Spiritomb}} who had knocked him out earlier. Though Grovyle is reluctant to help them (because the partner still does not trust him), he proceeds to tell his side of the story. The world's paralysis dated back to the present day, with the collapse of the Temporal Tower, governed by {{mdc|Dialga|2}}, the legendary Pokémon that controls time. When the tower collapsed, Dialga lost control of time, and it too lost all control. Dialga turned berserk, becoming [[Primal Dialga]]. Seeking only self-preservation, Primal Dialga tried to prevent history from changing, and hence its need to exterminate Grovyle and the team. The partner is visibly shocked by this revelation—and even more so when Grovyle reveals that he collected the Time Gears to prevent the tower from collapsing. Grovyle continues, claiming that the time stop caused by the removal of the Time Gears is merely temporary—the area affected would return to normal once the gears were placed in Temporal Tower. Grovyle then further revealed that Dusknoir is an agent of Primal Dialga sent to stop him and the team, and had everyone in the past played for fools.

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