The episode opens in a dream-like world, as Ash, Dawn and Brock are greeted by the lake trio. Suddenly, the dream world darkens as the lake trio runs away from a dark energy. Though Ash and his friends pursue, the energy bands catch up to the lake trio. Ash and his friends suddenly wake up, realizing that they all had the same dream.
The next day at Lake Valor, J's ship appears from its cloaking field and opens its ventral hatch, preparing the Galactic Bomb. Gary and his Umbreon spot the ship and reports to Professor Rowan over his radio. In Sandgem Town, the professor confirms through a live feed from his lab and decides to alert Yuzo and Professor Carolina at Lakes Verity and Acuity. Gary tries to stop the ship with Electivire, but Saturn's Toxicroak intervenes with a Dark Pulse, putting himself between Gary and J. Umbreon attempts to use Psychic, but Toxicroak quickly stops Umbreon with an X-Scissor attack before Umbreon can attack. Meanwhile, J sends the order to release the bomb. It descends into the lake's depths and explodes into a brilliant blue light, affecting Azelf. At the same time, Ash feels a sharp pain in his head, knowing that Azelf was affected and connects it to their dream. The bomb creates a gap in the lake, revealing an orb of blue light at the lake's bottom. Saturn mentions that the bomb was made from the Veilstone City meteorite and can open a hole in space connecting to where the lake trio live. While Professor Rowan fills Ash and his friends in on the situation at Lake Valor, Yuzo notices activity at Lake Verity, while Carolina notes activity at Lake Acuity. Back at the lake, Gary and Saturn observe the event, as J rides out on her Salamence.
Gary tries to intervene again with Electivire's Thunder, but a Poison Jab from Toxicroak stops that attempt. Team Galactic grunts release many Golbat to aid J as her Salamence fires Hyper Beam at the blue orb. The orb brightens and disappears, revealing the lake guardian Azelf. Surrounded by Golbat, Azelf fires Extrasensory to take down the Golbat, as they try to hit with Supersonic. Azelf dodges them, but Salamence blocks Azelf. J fires her bracelet at Azelf, and although it tries to block with Extrasensory, both attacks go through each other. While J and Salamence take the hit, Azelf is turned to stone and placed on a capture plate. Almost instantly, Ash feels the pain and they decide to head out. Back at Team Galactic headquarters, Cyrus and Charon observe the live events on screen as Cyrus recites the key part of the legend, revealing that if one of the lake trio members fall, the others would appear in short order. As predicted, his scouts at the other lakes reported brief sighting of the other lake guardians. Dawn and Brock both feel the cries of Mesprit and Uxie, and after talking with Rowan, decide to head to Lake Valor. Outside, Cynthia pulls up in a SUV. While Saturn takes the captured Azelf, Uxie and Mesprit arrive on scene, noticing their fallen comrade and try to free Azelf with Extrasensory attacks, but are forced to dodge Purugly's Shadow Ball and Skuntank's Flamethrower attacks. Jupiter and Mars have the Golbat attack. Both proceed to dodge before launching dual Future Sight attacks. The attacks go into the sky and dissipate, before J uses her bracelet to freeze Mesprit. Uxie fires another Extrasensory attack, cracking J's goggles. While Uxie smirks, J hits Uxie with the bracelet, freezing the final member of the lake trio, completing her mission.
Ash and his friends race to Lake Valor in Cynthia's SUV. Dawn and Brock also begin to feel sharp pain as Cynthia informs them that Looker is on Mt. Coronet and they need to contact him. Back at the lake, Gary watches helplessly as Team Galactic takes the lake trio. J and Salamence debrief and head back to their ship, preparing to head back to base. Suddenly, the Future Sight attack strikes and knocks out the ship's engines, sending it into the whirlpool. Inside, J and her crew brace as the ship hits the edge of the whirlpool and takes on water, the glass ports breaking and the ship descending into the depths before creating a huge explosion. Team Galactic makes their getaway in their chopper, leaving a frustrated Gary behind. Team Rocket rides in their balloon towards Mt. Coronet looking for Team Galactic. They spot Looker on the ground and land, to meet him. Looker informs them about the situation and tries to keep them quiet, wanting to stop them. Team Rocket decides to help. They notice Team Galactic security and plan to use a mimic disguise to get in.
Meanwhile, Cynthia drives Ash and his friends as Rowan informs Ash that Gary is okay, but Team Galactic got away. Cynthia brings up the Celestic Ruins and mentions that Team Galactic has everything needed to summon Dialga and Palkia, possibly unlocking powers beyond their comprehension. At HQ, Charon starts his experiment as the others watch. The Red Chain fragments are put into the stasis cells holding the lake trio, embedding the fragments on their foreheads and removing them from freeze, painfully drawing their power, which sends waves of pain through Ash and his friends. Suddenly, Ash and his friends are teleported out of Cynthia's SUV, causing her to stop.
Ash and his friends are suddenly pulled into Team Galactic's HQ, stunning everyone. They notice the imprisoned lake trio as Brock's Croagunk comes out, ready to battle its rival Saturn's Toxicroak. Mars and Jupiter summon Purugly and Skuntank, and everyone is ready to fight, but Cyrus calmly calls them out about human emotion hampering human advancement. Ash and his friends notice and find out that he is the leader of Team Galactic. Cyrus openly announces his intentions and plans to create a new world, Ash and his friends are not going to stand for it. Despite being surrounded, Ash and his friends decide to help, Pikachu and Piplup attacking the stasis cells while Croagunk attacks Toxicroak.
- 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.
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