When Ash, Misty, and Brock run to investigate a mysterious chorus of bells that spontaneously ring out, they chance to meet their old friend Morty and a Pokémon researcher of his acquaintance. Morty and the researcher discover that the sacred Crystal bells, which are said to ring when a legendary Ho-oh returns, are missing. Since the bells were also used to heal the Bug Pokémon living in that area, these Pokémon lash out against their human neighbors, covering the town with their webs. Ash and friends decide to get to the heart of things and, in the forest, find Team Rocket restrained by webs and hanging from a tree. Ash, Misty, Brock, Morty, and the researcher begin to battle with the Bug Pokémon. Just when it seems as if there is no hope an unsuspected ally appears.
Ash and his friends rest at the Ecruteak Pokémon Center and they discuss the route to Mahogany Town. All of a sudden, they hear a weird noise that's coming from the outside. They see Nurse Joy and Chansey run by. Nurse Joy says that there is something up with the Tin Tower. Morty notices this too, and is greeted by his friend Eusine. Both venture inside the tower to investigate, and they notice a set of gold bells are vibrating. They go up onto the ninth floor, which houses the special Crystal Bells, and notice that the bells are missing. Morty orders his Gengar to find the culprits. Meanwhile, Team Rocket celebrates their little steal in the surrounding forest, thinking that they will get some Legendary Pokémon now. James explains that when the bells ring, it is supposed to summon Ho-Oh. So, they start shaking the bells, but no sound is coming out. Jessie grabs them and swings them around, but one slips out and breaks on a rock. All of a sudden, an eerie wind begins to blow, and the Tin Tower's bells fall silent.
The group arrives at the Tin Tower, but Eusine blocks their path. Morty appears and is glad to see Ash again, remarking his arrival is almost prophetic. He informs Eusine that Ash saw a Ho-Oh when he first began his journey. Eusine instantly frowns at Ash. Morty takes everyone back to his place where he shows them all a scroll depicting the ancient Crystal Bells. He explains that the bells contained within the Tin Tower were recovered from the Burned Tower after it was destroyed 300 years ago. Eusine declares that the ringing of the bells today indicates that Ho-Oh still watches over everyone. He adds that Ho-Oh's anger will only melt away when the hearts of humans and Pokémon alike become one. Eusine explains that Ho-Oh sent three incarnations of the north wind, volcanoes, and thunder, to maintain the peace, Suicune, Entei, and Raikou respectively. Ash declares that he met Suicune, and he points it out in a book with confidence. Eusine is infuriated, having spent a lot of his time tracking Legendary Pokémon, and declares Ash a liar. He challenges Ash to a battle to prove his worth. Meanwhile, in the forest, Team Rocket is surrounded by angry Bug-type Pokémon. Meowth translates and reveals the wild Pokémon are angry at them for breaking one of the Crystal Bells. The Pokémon all fire a String Shot at Team Rocket.
Ash is confused as to why Eusine wants to battle him, but he accepts anyway. The match takes place inside the Ecruteak Gym. Eusine sends out Alakazam. Ash is not sure if he can win this one, but he tells Pikachu to start off with a Thunder Shock. Before Pikachu can attack, one of Morty's young apprentices rushes in and informs him that something is amiss at the Tin Tower. Everyone runs outside and they see that the Tin Tower is covered in webs. They rush towards the scene, but a group of Tangela stops them. An army of Parasect approach and the group retreats inside the Gym to avoid their potent Sleep Powder attacks. Ash and Eusine peer outside some windows where they notice that all of Ecruteak City is slowly becoming draped in webbing. Morty and Eusine refer back to the legend and fear that the stolen Crystal Bells has led to the current disturbances. They have no other choice now but to break through the Pokémon. Ash heads back out, but now the Parasect are much closer. Everyone else comes out, and Morty's Gengar pops in front and uses Confuse Ray on them, stopping them.
Ash has Cyndaquil use Flamethrower to burn through the String Shot webs. Gengar soon leads everyone through the forest to the stolen Crystal Bells, where they also discover Team Rocket entangled in the sticky threads. Morty rushes towards the bells on the ground, but he is nearly struck down by several Vine Whips from the Tangela. Brock notices that there are only three bells, and Misty demands answers from Team Rocket. Meowth remarks that Jessie broke the fourth one. Ash tries to reason with the wild Pokémon, but they are too angry to listen to reason. Spinarak and Ariados drop down and shoot a String Shot at them. Eusine sends out Alakazam, who uses Reflect to protect everyone. A Tangela strikes Alakazam down with a single Vine Whip, forcing Eusine to recall it to its Poké Ball. Ash tries to persuade the Pokémon, but a Tangela attempts to whip him as well. Just before the attack hits, something runs by that stops the Pokémon. Soon all the Pokémon start to flee from the area, and a shiny wind begins to blow, making the webs in the forest disappear. The Rocket trio is also freed from their String Shot cocoons.
The shadow appears and reveals itself as Suicune. Jessie, knowing that Suicune is a rare Pokémon, sends out Arbok in an attempt to catch it. However, Suicune just fires an Aurora Beam in response, sending Team Rocket blasting off. Suicune stands atop a cliff and stares at its surroundings. Now, Eusine finds this a good time to fulfill his dream of catching Suicune. He defies Morty's opposition and sends out his Alakazam. Eusine has Alakazam start off with Disable, but Suicune blocks it with a Mirror Coat. Alakazam follows up with Confusion, but Suicune counters with a Roar, sending Alakazam back into its Poké Ball. The momentary distraction allows Suicune to simply vanish into thin air, much to Eusine's frustration. Morty and the others turn their attention to the sky and notice a large rainbow, which Morty declares is a symbol of Ho-Oh. Ecruteak City and the surrounding forest subsequently become clear of the webs.
Outside the Gym, Morty exchanges a handshake with Ash and wishes him all the best with his future Gym matches. Misty notices that Eusine is missing. Morty explains that Eusine has already left to search for Suicune. With the Crystal Bells safely secured inside the Tin Tower, Morty hopes that Ho-Oh will make an appearance sometime soon. Meanwhile, Ash and his friends begin to trek towards their next destination, Mahogany Town.