Picking up from Losing its Lustrous!, Ash, his friends and Cynthia battle against Saturn and Mars in the Celestic Town Historical Research Center. Cynthia's Gastrodon manages to easily defeat the multiple Golbat sent out by Team Galactic. Ash sends out Pikachu and Chimchar while Dawn sends out Piplup and Pachirisu, to which Mars and Saturn counter with Purugly's Shadow Ball and Toxicroak's Dark Pulse. With help from Cynthia's Gastrodon and Garchomp, the attacks are repelled, but Chimchar is injured when it takes a Poison Jab meant for Pikachu.
This distraction allows Team Rocket to make their attempt to snatch the Lustrous Orb, only to be caught in the act by Officer Jenny. Despite both this and the fact they are surrounded by Galactic operatives, Team Rocket escapes after Cyrus gives a subtle order for Mars and Saturn to let them go. After they leave, Saturn sends the Golbat after them and flees, while the heroes are forced to retreat to the Pokémon Center to get help for Chimchar and Croagunk and so they can plan their next move.
Meanwhile, another Team Galactic Commander named Jupiter and her Skuntank use the Spear Key to find the location of the Lustrous Orb.
With police everywhere in Celestic Town, Team Rocket is left to flee to the Celestic Ruins, which were previously bombed by Mars. One of Saturn's Golbat spots them and goes to report back, along with Ash's Staravia who has also been searching for Team Rocket.
In the Pokémon Center, Cynthia advises Ash and his friends about the importance of the Adamant Orb and the Lustrous Orb, and their ties to Dialga and Palkia. Ash feels guilty for getting Chimchar injured but Cynthia, who has recognized Chimchar as the one that battled her under Paul's command, tells Ash that it is important not to regret the past but look forward to the future. Professor Carolina and Cyrus have since gone to the ruins to see the damage inflicted by Mars's attack, when Cyrus is informed of the whereabouts of Team Rocket by one of the Golbat.
Carolina and Cyrus find Team Rocket hiding in the ruins, and Mars—after disabling the police nearby with her Bronzor's Hypnosis—quickly arrives on the scene. She attempts to have Purugly and Bronzor attack Team Rocket, but Pikachu, Staravia, Piplup and Garchomp interfere as the heroes arrive. Trapped, Team Rocket tries a desperate move—threatening to destroy the Lustrous Orb. This only prompts Cyrus to explode in anger at them, lecturing the trio on the history of Sinnoh and the importance of the orbs in its space-time legend. Cyrus then loses his temper and begins laughing maniacally as the Golbat return to attack Team Rocket. They fail, but in the confusion Jupiter's Skuntank arrives and steals the Lustrous Orb.
That night at the Pokémon Center, Carolina apprises Officer Jenny of the day's events while Cynthia and Ash's group mourn their failure to protect the orbs. Cyrus advises them to not feel sorry for themselves, that they did an admirable job against Team Galactic, stating that he will remember them for their efforts before leaving.
The next morning, Cynthia departs Celestic Town to meet a challenger for the title of Pokémon Champion. The gang are worried about what Team Galactic are up to, but Cynthia tells them they should just proceed as normal, knowing they will all have to be ready for when Team Galactic make their next move.
Meanwhile, in the secret headquarters of Team Galactic, Mars, Jupiter and Saturn observe the Adamant Orb, Lustrous Orb and Spear Key, which they have attached to machines in a laboratory. A door opens to reveal the leader of Team Galactic—Cyrus. He admonishes Saturn for displaying ineptitude during the mission while Mars snickers. Cyrus then reveals that Ash and Dawn have witnessed the spirits of Mesprit and Azelf to his underlings' surprise. He orders Jupiter to head up the mission of collecting the lake guardians, to which he says she will contact the Pokémon hunters. Mars has news too—the Fuego Ironworks have completed their experiment on the meteorites stolen from Veilstone City, moving the Red Chain project into its final stage. Cyrus laughs insanely as he visualizes the 'beautiful and pure' world he plans to build with the immeasurable power of Dialga and Palkia.
- Message of the Wind is replaced by Surely Tomorrow as the ending theme.
- There is no Professor Oak's Pokémon lecture following this episode.
- The 97th episode of the previous anime series also featured the antagonists of that generation's games, much as this episode features the antagonists of the current generation's games. AG097, however, had a cliffhanger leading into its second part, while this episode is the final part of the two-part episode. The previous generation's arc, however, was the last appearance of the respective teams, while this arc, with four Badges left for Ash to earn in Sinnoh, is merely one of Team Galactic's biggest appearances.
- Music from Celebi: Voice of the Forest and The Rise of Darkrai is used.
- During the title card sequence, the former title card music from the Battle Frontier portion of the Advanced Generation series is played. The same applies to Losing Its Lustrous!.
- Prior to this episode's actual dub title being revealed, Cartoon Network had listed the previous episode's dub title with a "(Part 1)" attached, leading some people to believe this episode's dub title was "Losing Its Lustrous (Part 2)".
- Pokémon.com's listing lists this episode as "A Double Team Turnover" for an unknown reason.
- The dub title for this episode might be a reference to March Madness, as "Double Team" and "Turnover" are both terms used in basketball.
- Coincidentally, the episode also aired in the U.S. in March.
- While Cynthia's Gastrodon and Garchomp were battling Toxicroak and Purugly, Gastrodon's head was colored pink, instead of the usual brown.
- When Croagunk is recovering, his Japanese voice can be heard.
- When Chimchar is recovering, its tail is still alight even though it is asleep.
- Pikachu's Thunderbolt incorrectly comes from its tail, when it has been said many times that it stores electricity in its cheek pouches.