The Cerise Laboratory has just received a shipment of fresh vegetables sent to them by Laxton, a former student of Professor Cerise who left him to become a farmer two years earlier. Cerise tells Ash and Goh that Laxton has been having trouble with some Diglett and Dugtrio recently. As Ash and Goh express their eagerness to go and help, Chloe enters the room. Cerise reveals that he had asked Chloe to accompany the boys on this trip, which they happily agree to.
Ash, Goh, and Chloe travel to Laxton Farm, with the former two getting excited enough to run across the wide open countryside. Upon arriving at the farm, the group is welcomed by Laxton and his Voltorb, which shocks Chloe's Eevee for getting too close. Chloe happily greets Laxton, whom she knows from the time when he used to be her father's student. Before showing them the problem he's having, Laxton invites the children to taste some of his fresh vegetables. They try out some of the tomatoes he's growing, finding them extremely tasty. Laxton reveals that he crushes molted Golem shells to be used as fertilizer, explaining why his crops grow so well.
After the boys have eaten their fill of tomatoes, Laxton leads everyone to the biggest field on his farm, where he's currently growing carrots, with his Voltorb helping to fry away any unwanted weeds with its electricity. The troublesome Diglett then make their presence known, appearing all over the field in numbers too big for Voltorb to handle. Laxton explains that they started showing up not too long ago and are now ruining his ready-to-harvest carrots, which is why he asked Cerise for help. As the Diglett spend a lot of time hiding under the soil, Laxton says it's okay for them to pull out carrots to find them, since the carrots are due to be harvested anyway. Goh calls out for his Cinderace to help, and the group attacks the problem. Unfortunately, the Diglett, led and coordinated by a Dugtrio, are too fast for them to catch, and the Mole Pokémon all get away. Nevertheless, the group succeeds in harvesting a large amount of unspoiled carrots, earning a thank-you from Laxton. Retreating indoors for the night, they figure that if Dugtrio is the one leading the group of Diglett, catching it should solve the problem. Chloe realizes that the Diglett and Dugtrio were much better coordinated than they were, so they too should probably try having someone coordinate them to have better success. Ash and Goh suggest that Chloe should take on this role, and after a bit of hesitation, she agrees.
The next day, Chloe is standing on the balcony of Laxton's house, with four differently colored flags now marking each corner of the carrot field. Spotting a Diglett, Chloe directs Ash and Goh towards the direction it's going. The boys cut it off and pull out the carrot it was aiming for, allowing Goh to throw a Poké Ball at it as it surfaces and catch it. Dugtrio then shows up, and once again, Chloe directs Ash and Goh in the correct direction. With their partner Pokémon, Ash and Goh rush ahead of Dugtrio and pull out the correct carrot just as Dugtrio surfaces, allowing Goh to catch it before it can react. Without their leader, the Diglett grow confused and retreat. Another successful carrot harvest is made, and Laxton thanks the children for their help. They start wondering if the Diglett will now stop coming, and why they started showing up in the first place. Laxton says they used to live on a nearby hill, but had never come down to the fields before. The group decides to investigate the hill to see if they can figure out why the Diglett moved to the farm.
At said hill, Meowth is overseeing a small, unsuccessful field of crops, while Jessie, James, and Wobbuffet are relaxing nearby. Meowth berates Jessie and James for slacking off, as it is what had resulted in them running out of food and him having to resort to growing some in the first place, before calling in a Meowth robot to help water the crops. When the water fails to improve the crops' condition, Meowth figures that music could help them grow, and has the robot play loud music. Just then, Ash, Goh, and Chloe show up, immediately realizing that this loud noise is the reason why the Diglett had left their natural habitat. Noticing the twerps, the Team Rocket trio performs their motto, but the music is too loud for the group to hear anything the trio is saying, so Meowth has the robot stop playing the music and go away.
Deciding to punish the twerps for interrupting their relaxation time, Jessie and James declare that they'll use this opportunity to steal Pikachu, and have Pelipper drop them the Rocket Prize Master. They vend a pair of Poké Balls from it, which reveal a Drilbur and a Sandslash, while Goh sends out his newly caught Dugtrio to confront them. Dugtrio goes underground with Dig, and Drilbur and Sandslash do the same with Drill Run. A fierce underground battle ensues, although it naturally goes mostly unseen for those aboveground. Eventually, however, both of the Team Rocket's Pokémon are sent flying out of the ground, allowing Pikachu to tackle them with Quick Attack, before Goh has Dugtrio send them and the trio blasting off with Sand Tomb. As Goh goes to thank his Pokémon for a job well done, he notices that the battle made the ground really soft.
Back at Laxton Farm, Ash, Goh, and Chloe settle down to eat various carrot-based dishes that Laxton has made for them. As they eat, Goh notices the group of Diglett having returned and interacting with his Dugtrio. Understanding that the Diglett wouldn't fare well without their leader, Goh makes a choice and hands Dugtrio's Poké Ball to Laxton. He says he's fine with having just Diglett, and shows Laxton Dugtrio's Pokédex entry, which says that a field dug through and tilled by a Dugtrio is ideal for planting crops, making it a perfect partner for a farmer like him. Laxton is thrilled with this information, and happily welcomes Dugtrio and the Diglett to work and live with him.
As Ash, Goh, and Chloe head back towards Vermilion City, Chloe surprises the boys by excitedly running ahead of them, just like they had done to her while arriving. Ash and Goh happily run after Chloe, their teamwork at the farm having made the three even closer friends than before.