On its way from Eterna City to Celestic Town, a police plane carrying the Adamant Orb is attacked by Team Galactic and the Adamant Orb is stolen.
At the Celestic Town Pokémon Center, Brock and Dawn are packing to head out while Ash is perfecting a technique to counter Fantina's Hypnosis. News soon breaks about the Adamant Orb's theft, and the gang learns that the Adamant Orb was on its way to the Celestic Town Historical Research Center, which is currently studying the Adamant Orb's counterpart, the Lustrous Orb. They also learn that Cynthia is coming to Celestic Town, and decide to head to the Research Center to see her. Croagunk fails to stop Brock from hitting on Nurse Joy, instead choosing to stare out the window, a fact which gives Brock slight alarm.
Outside the Pokémon Center, Jessie, James, and TRMeowth ([[{{{2}}} (move)|{{{2}}}]]) plot to steal the Lustrous Orb before Team Galactic can.
At the Research Center, the gang meets up with Cynthia, who introduces them to her grandmother, Professor Carolina, head of the Celestic Town Historical Research Center. On a nearby rooftop, Saturn recognizes Ash and co. as the group that interfered with their plan to steal the meteors from Veilstone City, and warns Mars about them. Cyrus approaches the Research Center using his cover as a world-famous mogul while Mars and Saturn prepare their attack. As Croagunk once again stares off into space instead of stopping Brock from hitting on Cynthia, Ash and Dawn also take note of Croagunk's strange behavior. Team Rocket disguise themselves as police officers in order to gain entry into the Research Center.
Inside the Research Center, Professor Carolina explains the town's connection to Dialga and Palkia, as well as her own extensive research. Dawn and Ash recognize Mesprit and Azelf from a carving of the Lake Guardians (though they do not know their names), and relay their experiences with the two Pokémon. Cyrus suggests that Professor Carolina show Ash and Dawn the Lustrous Orb. In the Celestic Ruins, behind the Research Center, Mars' gang finishes setting up explosive charges.
Team Rocket, still in disguise as police officers, relieve the officers guarding the Lustrous Orb, but before they can sneak into the room, Officer Jenny leads Ash and co. down the hallway. Professor Carolina uses a key card and a palm scanner to open the room with the Lustrous Orb, where both Ash and Dawn examine the item, but feel nothing. This enrages Cyrus, who reveals that the Lustrous Orb may be directly connected to the dawn of time. As Cyrus tries to coax more information out of Ash and Dawn, Mars sets off the explosives, causing a panic within the Research Center. Professor Carolina finds that the door to the room with the Lustrous Orb won't reseal. The security system of the Research Center is revealed to have been compromised, which leads Cynthia to suggest moving the Lustrous Orb. Ash volunteers to help protect the orb, and Officer Jenny recruits the in-disguise Team Rocket to help, as well.
Saturn and his Toxicroak lead a team of helicopters to the roof of the Research Center. Brock's Croagunk releases itself from its Poké Ball and heads down a hallway, causing Brock to chase after it while the rest of the group takes the Lustrous Orb to the main entrance way, where Saturn is waiting. Saturn reveals that his Bronzor has put everyone outside to sleep, while his Toxicroak has taken care of everyone inside. Toxicroak, however, is shown to be in a face-off with Croagunk, and Brock realizes that Croagunk had sensed Toxicroak's presence all along.
Saturn tries to use Bronzor's Hypnosis attack, but Cynthia sends her Garchomp out to face it instead and it defeats it easily. As Officer Jenny and the others try to retreat, they find their path blocked by Mars. Just then, Croagunk falls through the skylight, followed by Toxicroak, who finishes off Croagunk with a Poison Jab. The episode ends as Cynthia prepares to release another Pokémon for battle.
