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As Ash and his friends continue to Blackthorn City, we see them still in the forest looking for a way out. Ash is still under Lily's Ashachu spell, but soon the spell wears off, Ash becomes human again, and everyone is relieved. Now, however, they still have a small problem; they are completely lost in the woods. Of course, Misty blames it on Ash as usual and insults him by saying she liked him a whole lot better when he was still a Pikachu.
While walking through the woods, Ash and his friends meet up with Jessie, James and Meowth in disguise. They proceed to tell Ash that his Pikachu loses energy because he's lost and they can recharge him with their new invention, the PikaPower Mach II. Jessie then rips Pikachu off Ash's shoulder and straps him in and radios to Meowth who swoops down in their balloon and takes Pikachu, Jessie, and James into the sky. Jessie then tells Ash to command Pikachu to use Thunderbolt. But the energy is absorbed into Team Rocket's machine, which also has the power to forcibly drain his victims of energy. Team Rocket threatens to sap all of Pikachu's power if Ash doesn't hand over the rest of his Pokémon, but Ash simply tells Pikachu to give all he's got. Soon enough, Pikachu's power overloads the machine and Team Rocket goes blasting off again. Ash happily catches Pikachu, but the power drain has left him exhausted.
Just then, a girl named Krystal meets up with Ash and his friends. Brock, of course, falls in love with her at first sight. However, Ash goes on telling her that Pikachu is badly hurt and that there isn't a Pokémon Center for miles around. She offers to help, but asks them to keep a very big secret for her in return, leading them up a large hill. As they walk, the group notices numerous Electric-type Pokémon climbing up the hill - Krystal tells them that they're all going there for a special reason. When they get to the top of the hill, they find a big lake, which Krystal claims has magical healing powers; the Electric-types come here to rest and recharge. She then orders Ash to put Pikachu into the water, and the Mouse Pokémon is soon good as new.
After Pikachu is healed, Krystal takes Ash and his friends out to the middle of the lake in a speedboat to show them the secret to the lake's power. When they look down from the bottom of the boat, they see what looks like an underwater temple with a crystal at the bottom. Krystal tells them how the Electric Pokémon have been coming to the lake for years, and how they are healed by the lake's power. She tells them a legend of how the temple supposedly sank underwater after torrential rains, unaware that Jessie, James, and Meowth are eavesdropping on the conversation...
As Ash and his friends discuss how the lake needs to be kept secret and how bad it would be if the wrong people got a hold of the crystal, Team Rocket goes underwater in a mechanical Tentacruel. They retrieve the crystal with little difficulty, but its light fades out, alerting Ash and his friends that something's up. The Team Rocket trio reveals themselves, reciting their motto before floating away in their balloon. As our heroes fume over this occurrence, the Electric Pokémon start to follow Team Rocket in attempt to get the crystal back. Ash orders Pikachu to Thunderbolt them, and the other Electric Pokémon join in the attack. However, Team Rocket sucks in their energy with the new and improved PikaPower Mach III. Gloating that their new machine is better than ever, the villains begin forcibly drawing energy from the Electric Pokémon, but black clouds appear in the sky, followed by a mighty screech and a huge bolt of lightning that breaks the circuit between the Electric Pokémon and the machine.
As everyone wonders what this means, the sky darkens and the clouds part to reveal the legendary bird Zapdos! Zapdos is extremely angry, flying towards Team Rocket to zap their PikaPower Mach III. However, even Zapdos loses energy and the heroes start to wonder why it doesn't seem to have much power in the first place. Team Rocket gloats, but Zapdos unleashes its full power and overloads the PikaPower Mach III, sending Team Rocket blasting off again. But then Zapdos falls out of the sky to the ground. Still angry and flailing about, it finally faints from weakness - clearly, it is in bad shape.
Krystal tells the group that this is the real secret - Zapdos itself often visits the lake to recharge itself. Needing the crystal to heal Zapdos, our heroes set off to find Team Rocket and the crystal. Pikachu senses the crystal is nearby, so they follow it to where Team Rocket had crashed. In an attempt to keep the crystal for themselves, Team Rocket sends out Arbok and Victreebel - although James again has to deal with the latter attempting to eat his head. Jessie orders Arbok to use Poison Sting, but Ash's Pikachu dodges and uses Quick Attack. With Arbok thrown into Jessie by the force of the blow, James orders Victreebel to use Razor Leaf - however, Ash tells Pikachu to use Quick Attack again, hitting Victreebel into its Trainer.
Ash demands that Team Rocket hand over the crystal, but Jessie instead throws Ash a Wobbuffet balloon, which inflates and bursts. Under cover of the resulting dust storm, Team Rocket makes a getaway in a new Wobbuffet balloon - in response, Ash sends out Bayleef and orders her to use her Vine Whip. Seeing the crystal being pulled from the balloon, James orders Victreebel to use its Vine Whip to get the crystal back. As the Grass-type-types struggle to break each other's grip on the crystal, Jessie orders Arbok to use Poison Sting. However, Pikachu uses Thunderbolt to blast Team Rocket off again, the crystal falling from their grasp. Running to catch the crystal, Ash dives off a cliff with Bayleef using her Vine Whip to catch him just in time.
With the crystal secure, Ash and his friends return to the lake, where Ash dives underwater and puts it back in its rightful place. He rises to the surface, but the crystal remains dark, so the Electric Pokémon swim over to the crystal and use their Thunder Shock attacks to charge it up. The group puts the injured Zapdos into the lake, where it sinks to the bottom - however, the crystal stops glowing before it can heal the Legendary Bird. The Electric Pokémon use Thunder Shock on the crystal again, which helps power up Zapdos as well. Fully recharged, Zapdos flies out of the water, releasing a mighty Thunderbolt that completely restores the crystal's glow. With the lake back to normal, Zapdos flies off into the clearing as everyone waves goodbye.
Ash and his friends are then shown ready to leave, promising Krystal that they won't tell anyone about the lake or Zapdos. Brock makes a last attempt to woo her, but Misty pulls him away by the ear; thus, the episode ends with everyone waving goodbye to each other.