At the Spear Pillar on the summit of Mt. Coronet, Team Galactic's leader, Cyrus, summons the Legendary Pokémon Dialga and Palkia, who appear though their portals. As they appear, the two Legendary Pokémon are tangled in the Red Chains. As the two struggle, while Commanders Mars and Jupiter watch from afar, Cyrus begins to reveal his plan about the creation of a new world, one that will have a new beginning, bringing the current world to an end.
At the Team Galactic HQ, Commander Saturn is observing the events from a giant screen. Cyrus then addresses Dialga and Palkia, ordering them to give him their power in order to create a new world, and as the chains around them begin to tighten, they glow, releasing their energy to create cracks in the stone pillars and ground beneath them, causing a Galactic Grunt's Glameow to dart back, surprised. As the world around them begins to end, Mars and Jupiter compliment Cyrus as they're closer to achieving Team Galactic's goal, but an angry voice orders them to stop. Turning around, they notice that Cynthia, the Sinnoh League Champion, has arrived in order to prevent Team Galactic from continuing with their plan as she orders Cyrus to release Dialga and Palkia immediately.
Spots of inky black start to cover the ground, growing larger and larger, creating vibrations that reach the Team Galactic HQ, until everything instantly comes to a stop. Everyone watches, waiting, but Cyrus smirks for a moment before watching a Pokémon emerge from the mass. The black, inky silhouette of Giratina's Altered Form rises. As all this occurs, the team back at HQ is watching, completely stunned. Cyrus refers to Giratina as the "Pokémon that comes from shadows", before having Dialga and Palkia attack it with Roar of Time and Spacial Rend, respectively. Easily dodging the attacks, Giratina retaliates with two Shadow Balls that destroy the Red Chains, allowing Dialga and Palkia to escape. Giratina then turns its wrath on Cyrus, seemingly engulfing him. Once the smoke clears, Mars and Jupiter are screaming for Cyrus as the find that he has disappeared, along with the strange Pokémon. Back and the HQ, Saturn desperately tries to make contact with Cyrus.
Lying on the ground, Cyrus comes around, noticing Giratina staring blankly at him. He begins commenting on the world he is now in and sarcastically asks Giratina if it is now satisfied after ruining his plans for a new world. Getting to his feet, Cyrus looks around at the strange world around him, realizing that there is nothing to this world, nor is there anything there, and that the world he desired is exactly like this one. Turning to Giratina, he smirks as he ponders.
Still attempting to make contact with Cyrus, Saturn finally picks up a signal and hears Cyrus saying that he doesn't want them to look for him. The signal is cut off, and Saturn's further requests for his boss's location don't get an answer. He finally takes off his headset, accepting Cyrus's final order.