Team Galactic has just stolen the Adamant Orb from a transport plane headed to Celestic Town, and their next target could be the Lustrous Orb stored in the town's research center. The research center is where Ash and his friends are headed, but they're just there to meet Champion Cynthia. She's back in town and meeting with her grandmother Carolina, the head of the research center. Cyrus, a well-known businessman with an interest in history, also joins the group to help protect the Lustrous Orb. But when he finds out that Ash and Dawn might have seen the Pokémon known as Lake Guardians, he has Carolina bring them to the Orb itself, which is under guard by a disguised Team Rocket!
According to Cyrus, the Lustrous Orb is connected to the dawn of time, but Dawn and Ash don't feel anything special when they look at it. Team Galactic chooses this moment to launch their attack, drawing out the security forces with a nearby explosion. They've also taken over the research center's security system, so Officer Jenny and our heroes try to escort the Lustrous Orb to a safer place. As they do, Brock's Croagunk runs away—it senses Commander Saturn's Croagunk and wants to fight.
Commander Saturn himself blocks our heroes' way, but Cynthia calls out her Garchomp to battle Team Galactic's forces and buy the others time to get away. Too late! Another Galactic minion, Commander Mars, surrounds our heroes. Ash and Dawn won't let them take the Lustrous Orb without a fight, but things aren't looking good. Toxicroak and Croagunk come crashing into the room, and Toxicroak knocks Croagunk out with one hit. Faced with Saturn's deadly Toxicroak and the combined forces of Team Galactic, Ash and Dawn might have no choice but to surrender the Orb!
On its way from Eterna City to Celestic Town, a police plane carrying the Adamant Orb is attacked by a horde of Golbat as well as a Toxicroak. The attack is led by Saturn of Team Galactic who notes that everything is going perfectly to plan.
At the Celestic Town Pokémon Center, Brock and Dawn are preparing to head out while Ash is perfecting a technique to counter Fantina's Hypnosis based on Dawn's Contest Battle the previous day. However, the training is put on hold when news soon breaks that the Adamant Orb was successfully stolen by Team Galactic, 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. Just then Nurse Joy arrives and Brock begins to hit on her; however, after a few seconds Brock gets the feeling that something is wrong and realizes that Croagunk didn't stop his misguided romantic attempts, instead choosing to stare out the window, a fact which gives Brock slight alarm. Meanwhile, outside the Pokémon Center, Jessie, James and Meowth decide 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 his friends as the group that interfered with their plan to steal the meteorites from Veilstone City, and warns Mars about them. Cyrus, a world-famous businessman who is responsible for many of the buildings and libraries throughout Sinnoh, approaches the Research Center 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 the Legendary Pokémon Dialga and Palkia, as well as her own extensive research. Dawn and Ash recognize Mesprit and Azelf from a carving of the lake guardians, and relay their experiences with the two Pokémon. Cynthia tells the gang that Mesprit represents Emotion and Azelf represents Willpower. Cynthia also tells everyone that there is a third lake guardian at Lake Acuity near Snowpoint City, Uxie who represents Knowledge. Brock realizes that Uxie is the Pokémon they heard about from May and Zoey during the Wallace Cup. Cyrus suggests that Professor Carolina show Ash and Dawn the Lustrous Orb. In the Celestic Ruins, behind the Research Center, Mars's gang finishes setting up explosive charges.
Team Rocket, still in disguise as police officers, relieves 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 and lands hard on the ground. Toxicroak follows and hits Croagunk dead-on with a Poison Jab, knocking it out while Brock watches helplessly on from the roof. Cynthia tells Team Galactic that they'll never be allowed to escape with the Lustrous Orb and releases another Pokémon for battle.