As Ash and his friends make their way through the forest, Clemont is excited about the Zapdos Festival in Joule Town and describes the local legend surrounding the event. A lightning strike startles the group as Zapdos itself flies through the stormy sky, catching the attention of everyone and getting them all excited about seeing Zapdos for themselves. Before Ash can stop him, Clemont begins to run towards the town where the festival will take place, but he is stopped in his tracks not a moment later by a tree collapsing after being struck by lightning. Noticing it isn't safe outside, Serena says it would be best if they find somewhere to take cover from the thunderstorm.
The group finds a cave and decides that they can use it to take shelter from the thunderstorm. Once in the cave, they get startled when they come across a strange man who is sitting inside with a broken leg. The man introduces himself as Stan. The group learns that Stan is a rescue worker who was driving out in the mountains when a lightning bolt caused a large rock to become loose and almost hit him, causing him to lose control and crash his van. He explains that he needs Ash and his friends to deliver some medicine to a hospital in the next town, and the group decides to help him. Noticing that they can't leave the cave due to the thunderstorm, Stan informs them that the cave leads to town, but a boulder is blocking the way. Ash sends out Hawlucha to break the boulder using Karate Chop and then sends out Noibat to help lead them through the cave with Supersonic, as Serena assists by sending out Braixen to light up the cave. Clemont promises Stan that once they get to town, they will send for someone to come and help him, to which Stan is grateful.
Making their way through the cave, the group approaches two tunnels through the cave, but Noibat uses Supersonic down both tunnels and discovers that the left tunnel is the way to go, allowing the group to continue to make their way through the cave.
Outside the cave, Zapdos is being chased after by a Ferrothorn mecha. It is soon revealed that Team Rocket is controlling the mecha and is attempting to capture Zapdos. After a failed attempt, Zapdos attacks them, destroying a rock as Team Rocket narrowly avoids it and makes their escape.
Due to the events occurring outside, the cave that Ash and his friends are in starts to quake, which causes a part of the cave ceiling to collapse, heading straight for Noibat. However, Hawlucha jumps and grabs him to bring him to safety. As the roof of the cave collapses, it creates a wall separating Ash and his Pokémon from Serena, Clemont, Bonnie, and Braixen. As Clemont asks if everyone on his side is alright, Serena becomes worried and shouts out to Ash and his Pokémon, and is relieved to know everyone is fine. However, Noibat is shaking with fear from the situation, but once Ash, Pikachu, and Hawlucha tell him everything is okay, he becomes much calmer. Hawlucha attempts to clear the rocks with Karate Chop, but Serena tells him not to once she notices that it could cause the cave to collapse and says that they will head to town together with Stan, leaving Ash to go alone to deliver the medicine.
As Ash, Pikachu, Noibat, and Hawlucha make their way through the cave, they come to another set of tunnels, to which Noibat again uses Supersonic to find the way out. Upon following the correct tunnel, they see the exit. However, not long after, they are attacked by Zapdos who was waiting outside, causing them to run back inside the cave for cover. Ash hears screams inside the cave and notices Team Rocket shaking from their encounter with Zapdos and, upon hearing another crash of thunder, becoming even more scared. As they run away, Meowth trips over and Ash confronts him, asking if they have something to do with why Zapdos is angry. Learning that they tried to capture Zapdos, Ash goes outside and attempts to calm Zapdos down, but Zapdos attacks again. Ash sends out Talonflame to battle Zapdos as a distraction so that the rest of them can make their way through. Talonflame puts up a good fight, but being at a type disadvantage, Talonflame gets knocked out, causing Ash to recall it. As Zapdos approaches again, Hawlucha volunteers to battle Zapdos himself so that the rest of them can escape. Hawlucha manages to hit Zapdos with High Jump Kick, which seems to deal a lot of damage, but Zapdos shows to be fine as it attacks Hawlucha with a super-effective move, causing Hawlucha to fall through the air.
Noibat flies off to save Hawlucha, and in doing so, evolves into Noivern. After catching Hawlucha and bringing him to safety, Noivern flies off again to battle Zapdos himself, using his newly-learned Boomburst. Realizing that Noivern can't seem to get close to Zapdos, Ash notices the large rocks around the area and tells Noivern to use the terrain to his advantage by using Supersonic to navigate around and outsmart Zapdos. This proves to be effective as Zapdos loses sight of Noivern and is hit by Boomburst, causing Zapdos to be slammed into a rock, which results in it falling through the air, which worries Ash. Just then, Team Rocket appears in their Ferrothorn mecha and captures Zapdos. Ash tells Noivern to save Zapdos by having him use Boomburst and orders Pikachu to fire a signature Thunderbolt, to blast Team Rocket off again, destroying the machine. Ash tells Noivern to use Acrobatics to free Zapdos from the ropes. Thankful to Noivern for saving it, Zapdos clears the stormy sky and flies away. With Zapdos now calm and the skies clear, Ash and his Pokémon continue their way around the mountain to deliver the medicine.
After his arrival in Joule Town, Ash says goodbye to one of the doctors after delivering the medicine and sets off to find his friends, who arrive a moment later. After finding out that everyone is alright, Serena and Clemont inform Ash that Stan isn't seriously injured and will be fine. Ash turns their attention to the top of the tree, to which Clemont, Serena, and Bonnie learn that Noibat has evolved into Noivern. As Noivern remains sitting in the tree eating berries, a fireworks display begins and the group sees Zapdos flying through the sky again. Zapdos itself starts sparking among the fireworks and then continues flying through the sky once more as Ash and his friends decide to enjoy the festival.