Ash and his friends are in Eterna City for Ash's next Gym battle, but first they have to help solve a heist at the Eterna Historical Museum! Someone has stolen the Museum's Adamant Orb, an artifact which is said to increase Dialga's power, and the security footage suggests a Sunflora was one of the culprits. Team Rocket stole the Orb with Meowth disguised as Sunflora, but it's the Pokémon bard Nando and his Sunflora that have been cornered by Officer Jenny! Luckily, our heroes and their recent acquaintance Gardenia, who turns out to be the Eterna Gym Leader, are ready to vouch for Nando's innocence.
This is a day for duplicates, because there's another Officer Jenny in town from Viridian City, too! Everyone splits up to search the Museum for the real culprit, with the Eterna City police especially eager to find the Orb first and uphold the honor of their department. But it's Piplup, Pikachu, and Nando's Sunflora who spot Team Rocket gloating over their theft, and soon backup is on the way.
Now that Meowth is no longer in the Sunflora costume, Team Rocket tries to bluff their way out of this jam. No such luck! But it's risky to battle Team Rocket while they're holding the precious Orb, so Officer Jenny from Eterna City has her Stunky stun Team Rocket with its powerful stench. Once Gardenia retrieves the Orb, it's a simple matter to defeat Team Rocket. Our heroes are then left to ponder the legends surrounding Dialga and Palkia... as well as the true motivation behind this attempted theft!
Ash and his friends finally arrive in Eterna City. But on their way to the Pokémon Gym, they hear the alarm going off at the Eterna Historical Museum, and the Eterna City Officer Jenny and her Stunky are summoned to investigate. The Adamant Orb has been stolen, and it shouldn't take a guess or two to figure out who's to blame—Jessie, James and Meowth (disguised as a Sunflora) of Team Rocket are the wrongdoers behind the theft. Ash, Pikachu, Brock, Dawn and Jenny arrive to confront the robbers, but Jessie calls out Seviper and has Seviper use Haze. The crooks disappear, but the exits lock off.
More Police officers rush to the scene of the crime. Gardenia arrives at the investigation, and Ash and his friends say hello to her. Lovestruck Brock is immediately taking notice, but Croagunk jabs him. Gardenia tells Ash and his friends what the police told her—the crooks used a Grass type to steal the orb. Officer Jenny arrives with her first suspect—Nando. Nando claims he isn't the crook because he came to the museum to study the history of the Sinnoh region. Gardenia believes Nando's story because she battled him earlier at her Gym. Officer Jenny doesn't believe his story, because she has a picture of a Sunflora (who was really Meowth in disguise) stealing the orb. Nando had a Sunflora with him, but it managed to sneak out of its Poké Ball before the police nabbed him. Nando is then brought in for questioning.
The Officer Jenny of Viridian City arrives and tells them it's her day off. The Viridian Jenny tells the Eterna Jenny that all Trainers with Sunflora must be investigated, and not just Nando, but the Eterna Jenny doesn't listen to her, and tells her not to get involved. Security Guards and Police Officers surround the museum. There wasn't a way for Team Rocket to get out with police everywhere, so they decide to fight their way out.
Gardenia explains that the orb Team Rocket stole was somehow linked with the Legendary dragons, Dialga and Palkia. Ash, Brock and Dawn set out to catch the crooks. Ash sends out Aipom, Staravia and Turtwig and Dawn sends out Piplup, Pachirisu, Buizel and Buneary and they send them to search for the crooks. Meanwhile, in the interrogation room, Nando keeps trying to tell Jenny he is innocent, but Jenny continues to refuse to listen to him.
Nando's Sunflora, after sneaking out of its Poké Ball, is walking around the museum. Two Security Guards spot Sunflora, and Sunflora Leech Seeds them. Sunflora soon runs into Aipom and Turtwig, and seeds them, too. Sunflora quickly ducks into the vents. Ash and his pals find Aipom and Turtwig seeded, while the Security Guards, after having somehow freed themselves from the Leech Seed, report to Officer Jenny. In the room Team Rocket is hiding in, the Security Guards take a look inside. Team Rocket hides on the ceiling so the guards won't spot them. Then, the guards leave.
Team Rocket drops from the ceiling. The vent Sunflora is in leads into the room Team Rocket is hiding in. Pikachu and Piplup have caught Sunflora, but Sunflora tells them the Sunflora in the room Team Rocket is in, is really Meowth in disguise. When Team Rocket removes their disguises and replaces them with new ones, they realize Sunflora is right! Piplup decides to attack, but Pikachu prevents Piplup from doing so. Pikachu runs back to tell Ash. Team Rocket spots Sunflora and Piplup, and Cacnea attacks them with Pin Missile.
Meanwhile, Pikachu is leading Ash and co. to Team Rocket. Team Rocket, still in disguise, walks past them, trying to act nonchalant. Sunflora attacks them with Cut, and their disguises fall off. Gardenia and Ash conclude that Nando's Sunflora isn't criminal, and that Team Rocket are the real criminals. After Team Rocket recites their motto and reveal they were hired to steal the Adamant Orb by another group, Ash and his friends demand they return the orb, but they refuse. Ash's Pikachu, Aipom, Staravia and Turtwig, Dawn's Piplup, Buneary, Buizel and Pachirisu, Brock's Sudowoodo, Nando's Sunflora and Gardenia's Turtwig surround them, but they can't use their attacks, because they could harm the Adamant Orb.
The Eterna City Jenny and her Stunky arrive on the scene and Stunky sprays Team Rocket, filling the room with its Stench. The orb falls out of Jessie's hands, and Gardenia's Turtwig quickly responds with a Leaf Storm. The orb lands in Gardenia's hands. Team Rocket makes a run for it while the Pokémon surrounding them are holding their noses, but the cops who were surrounding the museum have them cornered. The stink starts to spread outside the museum, forcing the cops to cover their noses and thus allowing Team Rocket to escape. After that, everyone outside is happy that the Adamant Orb is returned. Ash still wants to know the full legend of the creation trio, and Nando tells the group of the Original One, who helped shape the world by creating Dialga and Palkia before creating three other Pokémon to act as the world's spirit. Ash and Dawn are confused, the legend raising more questions than answers. Viridian Jenny poses another question that remains unanswered; who hired Team Rocket to steal the Adamant Orb. While everyone puts forwards familiar names (Butch, Cassidy and J being likely suspects), no-one can be sure who is responsible. For now the mystery will have to remain unanswered...
...meanwhile, high above Eterna City, a helicopter flies away from the city. Inside are members of a different, unfamiliar organization. The pilots remark what a mistake it was to entrust the bungling Team Rocket with stealing the Adamant Orb while their Commander sits in the back, unimpressed. Stealing the Adamant Orb will have to wait for another day.