Greenthumb Gardens is famous for its herb garden. Burdock is the current owner of the herb garden and is the richest man in town. He has many gardeners to tend it, including Carraway, who works for him as a servant. He lives in a servant's quarters next to the garden with his father and brother.
Burdock has a son, Dill, who is soon to be married to Lavender. Lavender's father has accumulated debt to Burdock and so she works as a servant to Burdock. However, Dill falls in love with Lavender. Marrying Dill would erase Lavender's debt. And so, they are to be married. However, Lavender is in love with Pepe, who spurns her advances. This makes Dill jealous. To add to this love triangle, one of the maids, Cayenne, is in love with Dill. She is jealous of Linda and tries to convince Dill that Lavender is being unfaithful to him.
Sometime before the people turned to stone, Klemens and Felix, former residents of Regenstein, warned the populace of the Grey Rain.
Soon after, Greenthumb Gardens is struck by the Grey Rain, much like Regenstein. This is caused by the Rainiac. The Rainiac turns everyone to stone. Carraway and Lavender were outside before the rain struck. When Carraway realized that the rain was turning everyone into stone, he covered Lavender with his body to protect her from the rain. However, they both turn to stone along with the rest of the town's residents.
The party enters Greenthumb Gardens to see its people turned to stone. They find the cause of the Grey Rain, the Rainiac. After defeating the monster, the party uses the Angel Tear from the top of Burdock's house and restores the people back to normal. However, Carraway, due to his overexposure to the rain, doesn't recover right away. His body is still stiff and he doesn't respond to anything. Lavender is horrified that Carraway, who previously had disregarded her feelings for him would try to protect her from the rain. Dill is jealous that Lavender is still spending more time with Carraway, even though he is ill.
During this time, Cayenne tries to advance on Dill and kisses him. Dill refuses to kiss back. She then tells him that what they are doing now is what Lavender and Carraway are doing as well. Dill refuses to believe her and storms out.
The party travels to Emberdale in the past to talk to Pamela. After telling her Carraway's symptoms, she is able to concoct some medicine to cure him. They return to Greenthumb Gardens with the medicine in hand. They feed it to Carraway who recovers from the effects of the Grey Rain. Everyone is excited about Carraway's recovery. To this end, Burdock holds a feast to celebrate Carraway's recovery and announce the engagement of Dill and Lavender. But Carraway is nowhere to be found. Burdock ask the party to look for him.
Cayenne is seen trying to convince Carraway to elope with Lavender so that she can have Dill all to himself. However, Carraway tells her that if he leaves with Lavender, his father and brother would suffer under Burdock. He leaves her after this conversation.
After witnessing the conversation with Carraway and Cayenne, Burdock starts to make his announcements. However, rain begins to fall. Fearing that it is the Grey Rain, the people return to their homes.
Carraway and Lavender have a conversation in the rain. Linda tries to convince Carraway to run away with her, but he refuses, not wanting to cause trouble for her or his family. Lavender becomes angry and tells him that when she marries Dill, she will work him to the bone. All Carraway says in response is that she should go back inside before she catches cold. She yells at him, telling him that she never wants to see him again.
Carraway decides to leave town. When the party tries to convince him that Burdock is a fair man and that running away would be cowardly, he responds that this is all true and that he should have done this a long time ago. But he says that it is too late for him. He leaves without a word to anybody.
The next morning, the party relays this message to Carraway's father, who thanks the party for telling him. Lavender, after learning about Carraway's departure, becomes depressed. Her tactics were actually geared towards making him elope with her. But they had the opposite effect. Dill is upset that Lavender still cares about Carraway even though he left her. Cayenne is mad at Carraway for not taking Lavender along with her. The party leaves Greenthumb Gardens with this resolution.
Dill and Lavender eventually marry and have a son, who Lavender calls Carrington. Burdock dies and sometime before the 30 year gap, Dill loses the mansion and the herb garden to Dan D. Lion and is reduced to a lowly worker. Cayenne marries Dan D. Lion and becomes lady of the house. Dill becomes lazy, starts to frequent the bars, and abuses Lavender. Lavender gets fed up with Dill so she leaves him and their son and becomes a nun. Cayenne, in the meanwhile, has been poisoning her husband via his food. He is withering to the point where he is bedridden.,
30 Years Later
The party cross El Magnifico de Puente Pomposo and head into Greenthumb Gardens. They notices that many things have changed since their last visit. Thirty years has passed.
They walk into the mansion and hear the maids are talking about throwing out the food that Cayenne has made. Camomile, one of the maids, decides to give the food to her dog since it would be a waste to throw out food. As she feeds it to her dog, Ginger, it becomes sick. This is when the villagers realize that the dog was poison. It is given an antidote by Herbie and it starts to recover. Camomile wonders how the dog became poison when she realizes that the only way that the dog could have been poison is if there was poison in Ginger's food. Camomile realizes that Cayenne has been poisoning the food for her husband and sets out to confront her.
Camomile confronts Cayenne about the poison. Cayenne pales when poison is mentioned, but she becomes defensive and tells the maid to drop the subject or else she would be fired. Camomile doesn't stop, though. She decides to reveal Cayenne's plan but she needs proof. She convinces the party to investigate Cayenne to see if there is any proof to validate her claims.
The party sees Cayenne leaving the mansion to see Dill. On the way, she drops a purple vial. In it is an addictive poison that causes the body to become weak, wither, and then kill the victim. The party give it to Camomile who gives it to Herbie, who confirms her suspicions. With the proof in hand, she goes to confront Cayenne again. However, Cayenne is preparing a meal for her husband, which is laced with poison.
Camomile brings her suspicions to Dan D. Lion's attention. He refuses to believe it until she shows him the vial which Cayenne carried around with her. Dan D. Lion recognizes it as the "medicine" Cayenne brought with him. Cayenne denies that it is poison, but Dan D. Lion tells her to drink the contents to prove that it isn't. It is at this moment that Dill arrives. He tells Dan D. Lion that Cayenne poisoned him and that he was her accomplice. Dan D. Lion throws both of them out of the town.
In the present, Greenthumb Gardens is an open field. Due to the prosperity of Wilted Heart, Greenthumb Gardens collapsed and becomes wilderness.
- Burdock - The owner of the Herb Garden, effectively making him the richest man in town. Burdock is a fair and just man.
- Carraway - A gardener in Burdock's garden. He is the future founder of Wilted Heart.
- Lavender - A servant of Burdock's. Her father owed Burdock money and Lavender has been paying it off ever since. Marrying Dill will erase her debt.
- Dill - Burdock's son. He is to be married to be Lavender. He is insanely jealous of Carraway.
- Cayenne - Burdock's maid. She is in love with Dill and wants Lavender, her competition, run out of town.
- Dan D. Lion - The new owner of the Herb Garden, 30 years later. He is being poisoned by his wife, Cayenne.
- Camomile - One of the maids in Dan D. Lion's house. She has a dog named Ginger.
- There is a pair of sisters in Greenthumb Gardens who are a reference to Maya and Meena, a pair of sisters from Dragon Quest IV. One of the sisters makes a reference to the other's quest to avenge their father..
- In the 3DS remake, all of the major characters in Greenthumb Gardens are named after various plants, particularly herbs, flowers, and spices.