Ash, Brock, and Dawn all seem to be having the same dream, in which the three Legendary Pokémon Azelf, Mesprit, and Uxie are calling them and asking them for help. When Pokémon Hunter J arrives at Lake Valor to catch Azelf on Team Galactic's behalf, Gary Oak is there to try and stop them. Unfortunately, Gary is unsuccessful, and Hunter J takes Azelf as a prisoner! Legend says that if one of the three Legendary Pokémon is taken hostage, the other two will appear. True enough-Mesprit and Uxie show up as soon as Azelf is captured. A powerful battle ensues, but Hunter J ultimately manages to capture all three Legendary Pokémon, and then gives the trio to Team Galactic. As Hunter J attempts to leave, Mesprit and Uxie unleash a powerful Future Sight attack, and Hunter J's ship goes down in flames.
Team Galactic now has everything it needs to call forth the Legendary Pokémon Dialga and Palkia. The process causes great pain to Azelf, Mesprit, and Uxie, as well as to Ash, Dawn, and Brock, who seem to be psychically connected to the three Legendary Pokémon. But Ash refuses to allow Team Galactic to continue, and our heroes begin a massive assault against them. The epic battle is just about to begin!
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 the former 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 to a stunned Gary that the bomb was made from the Veilstone City meteorite and can open a hole in space connecting to where the lake trio's unique dimension. Saturn exposits that the lake trio don't actually live in the three lakes - they merely observe the world through a portal to their dimension that looks like a lake. While Professor Rowan fills Ash and his friends in on the situation at Lake Valor, while both Yuzo and Carolina notes activity from their locations. 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. The Team Galactic Grunts send out numerous 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 them down, 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 HQ, 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 should fall, the others would appear in short order to restore balance. As predicted, his scouts at the other lakes report 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 her SUV, telling the heroes to get in. 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, knowing that Mesprit and Uxie have been captured. as Cynthia informs them that are going to meet with Looker, who is currently investigating on Mt. Coronet. Back at Lake Valor, 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 attacks strike and knock out the ship's engines, sending it into the whirlpool. Mars and Jupiter are stunned by the scene, while Saturn shakily notes how frightening the power of the lake trio is. Inside, J and her crew scramble to maintain control, but are unable to 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 Gary behind, who punches the ground in frustration.
Team Rocket rides in their balloon towards Mt. Coronet looking for Team Galactic but are frustrated with their lack of progress. 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. Though initially surprised, Looker is impressed, adding that he isn't to be outdone in the disguise department.
Meanwhile, Cynthia drives Ash and his friends as Rowan informs Ash that Gary is okay, but Team Galactic got away. Rowan advises the four to be careful and hangs up. Cynthia brings up the image depicted in the fresco at the Celestic Ruins and mentions that Team Galactic has everything needed to summon Dialga and Palkia, possibly unlocking powers beyond their comprehension. At Team Galactic's 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. Cynthia instantly recognizes what is occurring, the three wail in agony about how much more intense their pain is compared to earlier. Suddenly, Ash and his friends are Teleported out of Cynthia's SUV, causing her to stop, and directly into Team Galactic 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 are incensed that he has been the leader of Team Galactic all along. As Cyrus openly announces his intentions and plans to create a new world, Ash and his friends become infuriated at all the damage that Cyrus's vision has inflicted upon the world and Pokémon. Despite being surrounded, Ash and his friends decide to fight, Pikachu and Piplup destroying the stasis cells while Croagunk attacks Toxicroak.