On a hot day in Vermilion City, Ash and Goh are enjoying some shaved ice from an automatic ice-making machine, though Chloe cannot understand their enthusiasm. The device suddenly stops working. Next, they notice the lights inside the Cerise Laboratory are flickering and suspect it might be a prank by Ash's Gengar. Professor Cerise steps outside, greeting them with a smile as he announces that a strong pulse of energy has been detected, indicating a rare Pokémon has appeared. Goh then spots a dark thundercloud appear, and deduces that the Legendary bird Zapdos is coming. Cerise orders his research assistants to watch Vermilion Harbor, suspecting that Zapdos will arrive there shortly. Goh is determined to catch Zapdos and reveals that he has his Flygon on hand to help. Ash, however, argues that he will be the first to battle Zapdos, sparking a heated exchange between him and Goh. The thundercloud suddenly disappears and Zapdos fails to make any appearance leaving the boys disappointed.
The boys walk off, with Goh proposing the age-old question as to whether the Pokémon or Pokémon Egg came first. Ash is perplexed, though Goh asks himself if Zapdos lives in thunderclouds, or whether it creates them. He notes that no one has come up with a clear answer to such mysteries. They then see Chloe, who explains that she is waiting for a bus back home while her father is still trying to deal with the sudden blackout at the lab. Chloe adds that her house meanwhile didn't suffer a blackout, a detail that piques Goh's interest. Goh then gets a call on his Rotom Phone, with Professor Cerise announcing that more thunderclouds have appeared over the Harbor. Ash is keen to rush over to investigate, but Goh suggests they go in the opposite direction based on a gut feeling. They reach the Kanto Power Plant, an unmanned facility which supplies Cerise Laboratory with electricity. Ash is curious about Goh’s thinking, to which Goh, finally answering his earlier query, explains that the Pokémon comes first.
Inside, Goh literally bumps into Team Rocket, taking the boys by surprise. Ash is quick to accuse the trio of causing the power outage, but Team Rocket defends their innocence and replies that they were scouting the location as a potential second base. Goh isn't pleased to hear that they were up to another scheme anyway. A sudden cry, with Goh suspecting that Zapdos must be nearby, sends everyone into a frenzy of excitement. They soon discover that Zapdos has arrived inside the generator room. They watch in awe as Zapdos absorbs the electricity from the Power Plant, helping to explain the wave of blackouts back at the lab. Ash challenges Zapdos and selects Pikachu, Goh chooses Raboot, while Team Rocket summon the Rocket Prize Master to receive a Rhydon and Stunfisk. Zapdos quickly deals a blow, knocking Raboot and Pikachu down with a zap. Zapdos next tries to attack Rhydon and Stunfisk, but they withstand the attack as they are both Ground Pokémon. The revelation bolsters Team Rocket’s spirits, as Jessie orders Rhydon use Horn Drill and James calls for a Water Gun attack. However, Rhydon instead starts attacking the walls while Stunfisk’s attack is weak. Ash and Goh order Pikachu and Raboot to use Quick Attack, but Zapdos retaliates with some electric attacks. To overcome their tough opponent, Team Rocket and the boys join forces in a Raid Battle against Zapdos. The Legendary bird attacks again, but it misses its mark. As Raboot rushes forward with a Quick Attack, Jessie orders Rhydon to shadow Raboot's movements and block any oncoming attacks. James also offers assistance, having Stunfisk carry Pikachu on its back. Jessie calls for a Rock Blast next, but the attack, along with Pikachu's Thunderbolt and Raboot’s Double Kick, all fail to hit their mark. Zapdos escapes outside through the broken ceiling windows. Goh rushes to the elevator, hoping to reach the rooftop in time to continue battling Zapdos. Ash, however, is stopped in his tracks, as Team Rocket returns their focus to their original plan – to catch Pikachu. Ash orders Goh to go after Zapdos while he handles Team Rocket. Goh complies and reaches the rooftop to continue battling Zapdos by himself.
Suspecting that an aerial battle may unfold, Goh calls out his Flygon. The Mystic Pokémon approaches with Dragon Claw while Zapdos continue to unleash powerful Electric attacks. Goh orders a Dragon Breath attack next, which scores a direct hit on Zapdos. With that, Goh tosses a Poké Ball and Zapdos is temporarily trapped inside. The Ball rocks for several moments before Zapdos bursts out. Ash meets Goh up on the rooftop, having sent Team Rocket blasting off, and suggests Goh keep battling. The morale boost fuels Goh's next moves, as Goh orders Flygon to carry Raboot into the air. Flygon glides past the electric attacks with ease before ordering Raboot to attack with Double Kick. Raboot misses the mark and Zapdos retaliates with a direct hit of electricity. Flygon soars down just in time to break Raboot's fall, gently landing near Goh. Goh is frustrated by the setback, but Raboot gets back onto its feet and asserts that it is willing to continue fighting. Goh has Flygon and Raboot return to the skies. Flygon unleashes a Draco Meteor shower, and as Zapdos batters the projectiles away, Raboot moves in close using the Draco Meteor shower as stepping stones. Goh calls for another Double Kick, but Raboot learns a new move in its determination and instead strikes Zapdos down with a Blaze Kick. Zapdos hits the rooftop hard while Raboot lands on the ground. Goh rushes to help Raboot up, but Raboot orders Goh to focus on catching Zapdos first with its paw. Goh throws another Poké Ball, seemingly catching Zapdos. However, a sudden lightning strike thwarts his second attempt, shattering the Ball. Zapdos emerges once again, summoning a powerful thundercloud and retaliating with bolts of lightning. Pikachu is struck down by the lightning, but emerges uninjured and reenergized. Zapdos also rewards the wild Electric Pokémon that have gathered around the Power Plant with some voltage as well. Zapdos prepares to leave, and Goh resigns himself to the fact that a future rematch is in order with his Pokémon too exhausted to battle any further. He declares that the battle was fun and waves goodbye to the Legendary bird as it flies into the distance.
Returning to the lab, Professor Cerise and the boys review the new data on Zapdos. Cerise concludes that Zapdos probably used the Power Plant to restore its energy levels after being left exhausted from producing the thunderstorm seen over Vermilion Harbor. Goh is thrilled by the discovery, declaring that Zapdos not only creates thunderclouds but also lives inside them. Cerise adds that Zapdos can control electricity and gain strength from it as well. Professor Cerise thanks Ash and Goh for obtaining such invaluable information.