Ash, Dawn and Brock finally meet Azlef, Uxie and Mesprit. Suddenly, the space begins to be filled with shadows, as they consume the Lake Trio. After this, Ash, Dawn and Brock wake up, as they have dreamt the same dream. J, during the next day, is about to launch the bome Team Galactic have given her to get one of the trio. Gary contacts Prof. Rowan and reports J has appeared. Gary sends Electivire to get them, but Saturn's Toxicroak uses Dark Pulse to prevent them. Umbreon uses Psychic, but gets hit by Toxicroak's X-Scizzor. J drops the bomb and causes a bright blue light, making Azelf to be captured. Ash feels a sharp pain and knows Azelf is in trouble.
The spirit is captured; so Saturn explaines to Gary that the bomb is made from the meteorite they got and opens a portal to another dimension to get the Pokémon. Ash, Brock and Dawn contact Rowan to tell what happened. Rowan receives reports that the other lakes are shining a bright light. Seeing J passing by, Gary orders Electivire to use Thunder, but Electivire gets hit by Toxicroak. The member send many Golbat, while J's Salamance uses Hyper Beam on the light, causing Azelf to appear. The Golbat use Supersonic, but Azelf evades and hits them with a beam. J fires her own beam and while she has been hit by Azelf's own beam, Azelf is captured.
Cyrus recalls that when one of the trio is hurt, the others will come to help it. So, Uxie and Mesprit vanish, as they teleported. Ash, Dawn and Brock go to help the trio and go out and encounter Cynthia, who orders them to get in the car. While Gary wants to help, Toxicroak stands in the way. A light shines, as Uxie and Mesprit appear. They go to attack after seeing Azelf captured, but evade attacks from Mars' Purugly and Jupiter's Skunktank. They dodge the Supersonic and use Future Sight, but in doing so, Mesprit gets captured. Uxie fires a beam, affecting J and almost breaking her glasses, but also gets captured.
Brock and Dawn feel the pain as Ash did. Cynthia tells them they are to meet Looker, who is investigating at Mt. Coronet. Saturn, Mars and Jupiter thank J for the work and give her the reward and she goes away. J goes in the ship and departs, but the Future Sight of Mesprit and Uxie takes effect, as the air ship gets damaged. In a moment, the air ship falls in the lake and explodes. Team Galactic depart, leaving Gary angry at all this. Team Rocket fly in the balloon at Mt. Coronet. They spot Looker and come to him, lendning him help. Looker tells them Team Galactic might have spotted them and gets them behind a rock. He wants them punished to restore his reputation, so Team Rocket are more determined to help him.
Rowan reports to Ash, Brock and Dawn Gary is fine and tells Cynthia and them to be careful. Cynthia tells them that Team Galactic are available to summon Dialga and Palkia and use their power. Charon puts the gems of the Red Chain on the heads of the Lake Trio, causing them to pulse by a red light. Ash, Brock and Dawn feel the pain of the Trio and suddenly, they disappear; as they have been summoned to the place where they are. Though surprised they are here, Saturn sends Toxicroak, as Brock's Croagunk has called out by his own will. Mars and Jupiter send Skunktank and Purugly. As they are to battle, Cyrus stops them.
Looker tells Team Rocket they need to be cautious, but need to find a way to infiltrate. Team Rocket have dressed themselves aas Team Galactic, making Looker pleased, as he has a similar idea. Cyrus scolds his commanders, as they should not fight, as the emotions can possess one's heart and causing the person to fight, which will not make any progress for humanity. Cyrus tells the heroes they are in Team Galactic HQ and they are to prepare themselves for a new world. The heroes know he lied and stole the orb and demand the trio to be released, but Cyrus disagrees, but notices they might be important as they are linked to the trio. So, they all surround them to keep them.
Pikachu's Thunderbolt and Piplup's BubbleBeam cause the pods in which the trio is to be shattered. Croagunk fights Toxicroak, so the battle against Team Galactic begins.
- There is no Professor Oak's Pokémon lecture following this episode (due to it being shown immediately before The Battle Finale of Legend!).
- This is the first time that Mesprit, Azelf, and Uxie appear in their physical forms. They previously appeared as projected souls in Following a Maiden's Voyage!, Pruning a Passel of Pals!, and Uncrushing Defeat! respectively.
- The title card is read by Ash, Dawn and Brock.
- In this episode, J used a Galactic Bomb on Lake Valor, which is what Saturn did in the games.
- The background music Darkrai: From Within the Shadows from the tenth movie is used in this episode.
- Despite sharing the same name in both Japanese and English, Uxie has two different voice actors for both languages.
- Music from Celebi: Voice of the Forest, The Rise of Darkrai, and Giratina and the Sky Warrior is played during this episode.
- Team Rocket doesn't blast off or recite their motto in this episode.
- Gary's Umbreon looks much larger than it actually is in one scene.
- Both Mesprit and Uxie use Teleport during this episode, a move neither can legally learn.