As Ash and his friends take a rest alongside a dried river, they notice a strange light above the Remoraid Mountain. As they continue traveling, the light disappears as they arrive at the ruins of the Ancient Colossal Tree Tribe where they find Nurse Joy and a Remoraid Fossil. Nurse Joy explains that there haven't been any Remoraid in the area for centuries ever since the rivers and lakes dried up as a result of the actions of the Ancient Colossal Tree Tribe's Remoraidians who cut down the surrounding forests for the sake of building a large city. Eventually after all the land's natural resources dried up, the Remoraidians had to move away to find a new place to live, leaving the city deserted. Following this explanation, Nurse Joy then points out that recently, small flowers have been growing in the arid landscape again. After arriving at the Pokémon Center and having a drink, Nurse Joy reveals that there's an underground lake near the Pokémon Center which is filled up when water flows through the empty river bed approximately every 12 years. It is at this point that they meet Mr. Gan Gogh, an artist who visits once every 12 years to try to draw the Rainbow Lights.
Gan Gogh originally came across the Rainbow lights twenty-four years ago and he tried to draw them using seven different crayons, he was unable to get it right though. So twelve years later he tried using twelve crayons instead, which also was a futile attempt. However, this time he made sure to come prepared with a full arsenal of two hundred fifty-one crayons. Ash comments on how he saw the Rainbow Lights earlier before arriving at the Pokémon Center, which results in Gan Gogh asking Ash where he saw the lights from. When Nurse Joy subsequently maps out where the lights must come from, it is determined that their origin is as the place formerly known as Remoraid Lake. Brock then brings up a legend he heard about the Remoraid at the lake being very difficult to catch, resulting in Misty asking how can Water-type Pokémon be living in an empty lake anyway. After this question is posed, Team Rocket arrives posing as archaeologists, with Meowth disguised as a Mummy. After this unexpected arrival, the lights suddenly appear in the sky again, however are gone before Gan Gogh has time to choose a crayon to start with.
Following this, Ash, Misty, Brock, Gan Gogh and Team Rocket all decide to go examine the cause of the lights over at Remoraid Lake, and along the way they notice that there is more plant life the closer they get. Finally upon arrival at the lake they discover a strange crystal-like tower, which Team Rocket decides could have potential monetary worth before discovering it was made of ice. They then decide that since there's nothing better to do, they should go back to their usual plan of stealing Pikachu, which James succeeds in doing by sneaking up from behind and grabbing him with rubber gloves. Ash is ready to battle Team Rocket, however Gan Gogh steps in first with his Venusaur. Gan Gogh's Venusaur easily defeats Jessie's Arbok, retrieves Pikachu and sends Team Rocket blasting off with a Solar Beam.
As the sun rises after the battle, water suddenly starts shooting out of the ground within the lake bed, as a group or Remoraid appears using their Water Gun and Ice Beam attacks to enlarge the ice pillar in the middle of the lake. Misty decides to attempt catching one of the Remoraid, but fails due to them suddenly swarming together as the Poké Ball can't work on more than one Pokémon at once. However, it is proven by Team Rocket who has just returned in their balloon, that Poké Balls aren't the only way to catch Pokémon by using a net instead. This also fails though, as the Remoraid all use their Water Gun to propel themselves higher, breaking a hole in the balloon and escaping from the net as Team Rocket blasts off again. As the pillar of ice then starts to melt, the rainbow lights appear in the sky again due to refraction of the sun's rays through the evaporating water vapor as the rivers begin to flow again. Later, Ash comments on how Gan Gogh never got the drawing he was hoping for, however he says that the fond memories that he has of this experience are worth more than any drawing will ever be. And so, our heroes continue their journey as they leave for a new adventure.