Our heroes are going along a harsh desert like landscape and they need to get some water. Team Rocket is also there and they need water too. Brock sees some mysterious lights over Remoraid Mountain, but they disappear soon after. Team Rocket also sees the lights and they try and follow it, but they also disappear. The brats decide to go to the Pokemon Center to cool down and get some water and Team Rocket follows along. On the way, Ash and friends find a historic Pokemon city and a Remoraid fossil. Nurse Joy suddenly walks up and explains that the Remoraid have all disappeared since the water dried up. She then tells them that the Remoradians cut down all the trees and abandoned the land because it turned into a desert.
Before they go to the Poke Center, they see some pink flowers growing on the ground, which is quite strange because they are in the desert. Joy invites them back to the Pokemon Center to get some water and Team Rocket follows. As not to be noticed, Team Rocket disguises themselves as Pokemon archeologists and they have some water too. Joy shows everyone that she gets the water from a mysterious lake below the Pokemon Center.
Suddenly an old man named Mr. Gango starts talking about the mysterious rainbow lights. He says that he saw them and tried to make a sketch of them, but he didn't have the time or the colors. He continues to say that the lights show up every 12 years and that this time he is going to try and capture all the colors.
Ash and friends explain that they just saw the lights over Remoraid Mountain, but Team Rocket (in disguise) interrupts and says that they're uncovering the ruins. Gango suddenly sees the lights again and tries to capture them, but he gets his colors mixed up and the lights disappear again. They decide that the best thing to do is go to Remoraid Lake and see what causes the light. The strange thing is, the closer they get, the more flowers and grass they see. When they finally get to the top, they see a tower made totally of crystal, but Meowth licks it and finds out that it is only ice.
Team Rocket then grabs Pikachu and they recite their usual lines. A battle ensues, but Gango stops Ash from battling because he doesn't want the light to be ruined. Gango helps by sending out his Venusaur who rescues Pikachu and sends Team Rocket blasting off again! Gango then explains that he went from trainer to Pokemon artist, so that's why he has the Venusaur. When the light finally comes up, they see that the Remoraid use their Water Gun and Ice Beam to make the giant pillar of ice. Misty like a fool tries to catch one of them, but they all come together and block the Poke Ball.
Team Rocket then comes back and catches all the Remoraid in a giant net. Ash is about to save them, but Gango tells him that the Remoraid can get away themselves and he is right. The Remoraid break the net, pop the Meowth balloon and get away sending Team Rocket blasting off for the second time. They find out that the lights are created by water vapor reflecting the colors. The river then suddenly gets all the water back and the Remoraid burrow into the mountain. As Ash and friends are leaving, they look back and see the beautiful lights for one last time before moving onto their next adventure