Team Galactic Commanders Saturn and Mars have cornered Cynthia, her grandmother Carolina, the business mogul Cyrus, Officer Jenny's team, and our heroes inside the Celestic Town research center. A battle erupts as Saturn and Mars try to steal the Lustrous Orb, but Cynthia's Gastrodon, Ash's Chimchar, and Dawn's Pachirisu defend our heroes against Mars' Purugly and Saturn's Toxicroak. But during the fight, Chimchar is badly hurt by Toxicroak, and Team Rocket—who were disguised as Jenny's police officers—manage to grab the Orb and escape! Team Galactic leaves, but Ash and his friends can't pursue them; first, they must tend to their injured Pokémon.
Ash's Staravia and Cynthia's Garchomp search for Team Rocket while our heroes rest at the Pokémon Center and try to figure out Team Galactic's plan. Are they planning to use the Lustrous Orb to help awaken Dialga and Palkia? In the meantime, Team Rocket hides out in the ruins near the research center, but they're soon spotted by Garchomp and Staravia—and Carolina and Cyrus, and even Team Galactic! As all sides converge on the ruins, Cyrus begins ranting about the power of the Lustrous Orb, just before Team Galactic's Golbat swarm the area. In the confusion, a Skuntank grabs the Lustrous Orb, blasts Team Rocket into the sky, and brings the Orb to Commander Jupiter, another Team Galactic member.
With the Lustrous Orb in their possession, Team Galactic uses the Golbat to cover their escape. Our heroes try to give chase, but it's useless—Team Galactic gets away scot-free. However, Cynthia has begun to suspect Cyrus and his crazed rants. Although she doesn't know it, Cyrus is in fact the head of Team Galactic. After he leaves Celestic Town, he joins his minions at Team Galactic's base and reveals his plan for the Adamant Orb and Lustrous Orb. Using the Orbs, and the help of a certain Pokémon hunter, he's about to launch a plan that will let him to summon the Legendary Dialga and Palkia!