In the Johto region, a storm mixes up a lake's waters, causing it to become muddy and brown. However, the Legendary Pokémon Suicune appears and uses its powers to make the water crystal clear again. The news of Suicune being sighted quickly reach the ears of Professor Cerise in Kanto, and he relays the information further to Ash and Goh. Chrysa and Ren, however, point out that multiple sightings of Suicune have been made around the same lake, which is unusual, as it tends to move along after purifying a body of water. As such, Professor Cerise dispatches his research fellows to the site to investigate.
After arriving in Johto, Ash and Goh head to the lake where Suicune was sighted, but as they approach it, a disgusting smell reaches their noses. At the lake, they find out that it's thick with garbage and pollution, despite Suicune having been supposed to have purified it. Nearby, they spot a group of men dumping pollution and having their Pokémon use Sludge Bomb into the lake. Goh plans to contact Officer Jenny, but Ash rushes ahead to confront the polluters before Goh can do so. A battle almost breaks out between the two sides, before a man the polluters refer to as their boss arrives, pointing out that Suicune has appeared. Once again, Suicune's powers clean the lake, and it attacks the trucks that were dumping pollution into it. The boss, however, is not worried, as he sees that Suicune's repeated use of its powers has left it low on stamina. Ash realizes these men are Pokémon hunters, and Goh understands they purposefully polluted the lake multiple times in order to force Suicune to use its power repeatedly and leave it weakened for capture.
The hunters have their Pokémon bombard Suicune with Sludge Bombs, with one of them keeping Ash and Goh from approaching as Suicune is tied down with ropes and nets. Desperate to come up with a way to save Suicune, Goh pulls out a Poké Ball and tosses it at the Legendary Pokémon, sucking it in. The Ball lands back into his hands, shaking three times before Goh's Rotom Phone reports a successful capture, much to everyone else's astonishment. The hunters, displeased of having their hard-worked catch being taken away from them, intend to take it back by force. Ash calls out Lucario and urges Goh to run away while he battles the hunters. Goh agrees and flees to get Suicune to a Pokémon Center. However, in the middle of his escape, he ends up tripping and dropping Suicune's Poké Ball. The Aurora Pokémon emerges and glares at Goh, displaying a very clear distrust towards him. Goh tries to convince it to come to a Pokémon Center with him, but it simply freezes its Poké Ball with Ice Beam and climbs up to a nearby tree to rest. Goh climbs up after it and finds several forest Pokémon standing before Suicune in an attempt to protect it, as it had cleaned the lake up for them. Goh tells them he's not one of the hunters and leaves his Cinderace and Alolan Exeggutor to watch after Suicune as he heads off with Sobble and Raichu. Ash, meanwhile, has managed to lose the hunters and wonders how Goh is doing.
Goh eventually returns to the tree, with his Raichu handing Suicune some Pecha Berries to cure the poison the hunters inflicted on it. The Berries work, and Goh also gives the forest Pokémon some other Berries to eat and for Suicune to regain its stamina. The hunters inform their boss that they've managed to relocate their catch and move out to reclaim it. Meanwhile, Goh notices an injury on Suicune's back leg and uses a Potion to treat it before wrapping a cloth received from Chloe around it. Just then, Goh's Exeggutor alerts them that the hunters are arriving. Goh engages them with his Cinderace and newly caught Drowzee, which he had captured in order to fight the hunters' Poison Pokémon more effectively. Although Goh manages to hold his own for a while, the hunter boss then sends out his Houndoom, which easily defeats Drowzee with a single Crunch. The hunters seize Suicune in a net and pull it down from the tree, beating it up as Goh begs for them to stop. Just then, Ash returns to help, and the two engage the hunters together. Although Cinderace ends up getting poisoned as well, Goh refuses to give up. Just as the boss tries to finish Goh off with Houndoom, Suicune, having observed Goh's determination, breaks free from the net and agrees to battle by his side. With a series of Hydro Pumps and an Ice Beam, the hunters' Pokémon are defeated, and another Ice Beam freezes the hunters into a block of ice that Officer Jenny picks up and carts off soon after.
With the hunters dealt with, Goh places Suicune's Poké Ball on the ground and tells it to resume its important journey. However, as Suicune emerges from the Poké Ball, it looks at Goh in the eye for a moment, before willingly returning to its Ball, showing that it wishes to stay with him. Thanking Suicune for its decision, Goh brings it back to the Cerise Laboratory, where Professor Cerise, Chrysa, and Ren are astounded to see Goh having actually caught the Legendary Pokémon. Suicune races to a hill in Cerise Park and unleashes a powerful gust of wind that forces everyone to shield their eyes. As the wind dies down, Suicune has disappeared, but Goh says that it's still there, even if they can't see it.