Ash, Misty, and Tracey are still walking through the desert when Ash asks if either of them are hungry. Misty sighs, and Tracey points down a hill. Below them is the city of Trovatopolis. They stand in place, marveling at the huge city. Nearby, Team Rocket watches Ash and his friends from behind a rock. They review their latest plan to capture Pikachu using, you guessed it, a hole. Jesse and James stand up and start to say their motto, but are brought down by Meowth. He tells them that Ash and his friends will hear them, and that they need to make it a surprise attack. James pulls out a remote and pushes the plunger. Nothing happens for a moment, then a big hole forms under them. They fall, screaming.
Misty hears these screams, and all three stop to listen. The reverberations from the explosion cause another hole to open underneath them, and they fall down to the depths below. They land unharmed and, after Ash and Misty help Tracey get his head stuck out of the ground, set off to find a way to get out. They follow a tunnel and wind up in the sewer system for the city. They then start to look for a manhole cover in the ceiling so they can climb out. As they walk, Ash hears the tinkling of a bell. Something taps him on the shoulder, he turns, but sees nothing. He turns back to his friends, but they're staring in horror at something behind him. He turns again and sees a huge tentacle poking out of the water. Pikachu prepares to shock it, but Misty reminds him that they'll get shocked too (so what? They probably would've even if they weren't in a watery environment). Ash agrees and sends out Bulbasaur instead. Its Razor Leaf attack is batted away, and the tentacle pulls Bulbasaur into the water. Ash starts to dive in, but is held back by Misty and Tracey. As he struggles to release their grip, a circle of light appears above them. They look up and see Officer Jenny's head. She sends a rope down and, after tying Ash to it so he won't go looking for Bulbasaur, they climb up.
At the police station, Ash and his friends are put into a jail cell. As Ash pounds on the door, Tracey and Misty speculate as to why they're in there. Suddenly, the door opens and Officer Jenny steps in. She tells them that they can leave, but before they can do so, a rather large man steps in. Officer Jenny rather unhappily welcomes him, addressing him as the Mayor. She tells him that Ash and his friends had just gotten into town, but he asks her to keep them in the cell for a week. She can't, so he tells Ash and his friends not to tell anyone about what they saw in the sewer. They protest, and the Mayor threatens to charge them with endangering public safety. Jenny tells him that they can't keep the creature a secret forever, and explains to Ash and his friends what has been going on. Apparently, there have been a lot of sightings of this strange, tentacled creature lately. All of them have involved the stealing of food, but that the Mayor feels that if the public hears about it, they'll panic. They'll never catch it, for there's almost 500 miles worth of sewer under the city. The Mayor adds that there's an election the next week and his chances at staying mayor will be ruined if word gets out.
Just then, Nurse Joy walks in. She tells the Mayor that he can't go through with the plan that he has formed. She tells Ash and his friends that he plans to kill the creature instead of capturing it and studying it. Officer Jenny tells him that the plan is illegal and he storms out. Ash and his friends go back to the Pokémon Center with Nurse Joy to call Professor Oak. He agrees with them, saying that it could be some new species of Pokémon or a Pokémon that has undergone some sort of mutation. He tells them to try to prevent the Mayor from killing it, but Nurse Joy tells them that all he currently cares about is getting reelected. Ash and his friends walk out of the Center and see what she meant. There are posters of the Mayor everywhere and even a statue of him in front of City Hall. They see an odd picture on the base of the statue and decide that it must be the Mayor's logo. Ash tells them that they need to go find Bulbasaur and they rush off.
They stop when they see the Mayor addressing a large group of uniformed men. They listen and hear that what Nurse Joy said is indeed true. Ash tells his friends that they need to get into the sewer before the men do, or else they'll never find the creature or Bulbasaur. They go back to find Nurse Joy, and she leads them to an opening in the side of a reservoir that they could get into. Ash tries to climb up to it, but slides down the side
Meanwhile, Team Rocket has been wandering around, looking for a way out of the complex sewer system. They complain about how hungry they are. Meowth hears a bell, and feels a tickling sensation under his chin. He thinks that it was Jessie or James petting him, but it turns out to be the creature's tentacle. They hurry off and don't stop for a while. When they do, they hear footsteps, and a figure rounds a corner. James sends out Weezing, who fills the area with a Smoke Screen. They run off and leave whatever the figure was coughing. The smoke clears, and we see that it was Ash and his friends. Tracey says that he could've sworn that those people were Team Rocket, but the thought is chased out of their minds when they notice Togepi is missing. They look around, and Misty sees it walking towards the water. She grabs it, and looks back at her friends. When she sees the looks on their faces, she looks in front of her again. Needless to say, the tentacle is there (y'know, this is all we've seen of this creature, and it doesn't really look like a tentacle). It tries to grab Togepi, but pulls Misty in with it. Ash sends out Muk (Muk!! Oh boy!) in order to find her, but it jumps onto Ash in happiness to see him. Team Rocket has once again slumped to the ground in fatigue and hunger. They hear the creature again, and decide to try to scare it. They make weird faces and run around the corner, only to see the Mayor's SWAT team. As they stand there looking at each other, one man asks the mayor over a walkie-talkie what they should do. He tells him to attack, and they all start firing large pellets of goop at Team Rocket. They run off. Muk has been leading Ash and Tracey around during this time, and they come to a wall. Muk points into the water, and they can see that the tunnel continues under the surface. They take a deep breath and swim through it. Ash surfaces first, and sees the tentacles waving in front of him. He yells in fright.
The Mayor's men come out of the sewer and report to him. They tell him that they didn't see the creature the Mayor was looking for, but that they did see three others (Team Rocket). He tells them that they need to block every way into the sewer with cement, and work starts immediately. Back with Ash and his friends, Ash comes to and sees Misty, Pikachu, Muk, and Bulbasaur looking at him. He hugs it in happiness, but is startled to feel the tapping of the tentacles again. He looks over, and sees a large Bulbasaur with its vines out. It's been it all along. Ash wonders aloud how it got there, and Tracey points out that it's wearing a collar. They get a closer look at it, and see that it's a bell with the Mayor's special symbol on it. Meanwhile, Nurse Joy is yelling at the Mayor. He defends himself by saying that now they don't have to worry about the creature. She reminds him that Ash and his friends are still in the sewer, and he tells her that he'll let them out after the next election. Nurse Joy protests, saying that the election isn't for another week, but the Mayor just shrugs it off.
Later, the Mayor enjoys a bath. He hears a loud rumbling sound and his tub is suddenly blown off the floor. Water gushes out, as does Ash and his friends and the large Bulbasaur. The Mayor floats out in the tub, and is thrown to the ground outside. He gets up and Ash asks him if he recognizes the big Bulbasaur. He looks at its collar, and thinks back to when he was a kid. He had a tiny Bulbasaur back then, but let it loose into the sewer when it wouldn't evolve. The Bulbasaur doesn't seem to mind, as it happily lifts the Mayor up in its Vines. Unfortunately, since the Mayor is dressed only in a towel, and people are starting to gather, he gets very embarrassed.
Misty tells the Mayor to apologize to his Bulbasaur, but he refuses. His men run up, and he tells them to attack it. Ash intervenes with a Thunderbolt, and his Bulbasaur Vine Whips them into the sky. The big Bulbasaur follows the lead and flings the Mayor into the air. He lands on his statue of himself, and it breaks. Later, Officer Jenny and Nurse Joy thank Ash and his friends for everything that they did. Ash asks them about the gym on Trovita Island, and Nurse Joy points out to sea. Only a little ways away, they can see a small island. Officer Jenny offers to take them to the pier so they can take the ferry to the island and Ash accepts
But wait! What about Team Rocket? They've found a grating that they can see out of, but can't figure out how to get out. They sigh, and Jessie sneezes. The bars fall out, and they cheer. You were lucky, Team Rocket!