When researching her family tree for someone who isn't a total boob or criminal, Lisa finds the 1860 diary of Eliza Simpson, a young girl who was in the Underground Railroad and tried to help a slave escape to Canada, but a diary by one of Milhouse's ancestors casts doubt on just what Eliza accomplished.
Miss Hoover tells her class that their assignment is to research their family tree, which makes Lisa excited to do the assignment, because she is anxious to find out her heroic ancestors. However, Lisa finds out that all of The Simpson ancestors are horrible and not heroic at all. Each and every one of her ancestors were crooks and murderers. Lisa says there has to be a good ancestor, and she asks Grampa if he knows any, however, he only tells about Abigail Simpson, known as "The Pittsburgh Poisoner." Lisa states that she will not give up and that somewhere in the Simpsons' genealogy there is a noble spark and that she will find it, even if she has to go back to Adam and Eve.
Lisa searches up in the attic for some help, and finds "The Diary of Eliza Simpson" in a crate. When she begins to read the diary, she learns Eliza is going to get a slave, and is forlorn to realize that the Simpson family descended from slave-owners. However, Lisa later learns, after reading more of the diary, that Eliza was going to Colonel Burns' ball to help his slave, Virgil, escape to freedom. Homer tells Lisa that she should stop reading the diary now, because when she learns the whole truth, she may not be able to bare it, and then puts the diary in the vent. However, Lisa must know the whole story, and takes the diary out of the vent and continues reading. She reads that Eliza and Virgil were caught by patrolmen, and that the horses were too fast for them. However, after reading the last sentence of the page, Lisa turns it, but discovers that the rest of the diary is completely dust. Santa's Little Helper approaches the diary and then sneezes, destroying the whole thing. Marge tells Lisa that she may be able to find out the rest of the story at the library. At the library, however, they have nothing on Eliza Simpson, but the cookbook by her mother, Mabel Simpson. They then learn that Eliza and Virgil made it back to the Simpson home after disguising Virgil as a clown in the circus and Eliza as the youngest bearded lady. Lisa then learns that Eliza's father, Hiram, didn't want the slave in the house because it would get him in trouble with Colonel Burns. However, after tasting Virgil's 'cakes', Hiram swears that he will help Virgil escape to Canada for freedom.
Lisa is then excited to learn that the Simpson family did have heroes, and presents her story to the whole school. But when she ends her presentation, Milhouse tells her that he obtained the journal of his great-great-great-great-great grandfather, Milford Van Houten. Lisa learns that Colonel Burns came to the Simpson home due to suspicion and demanded Hiram to tell him where Virgil was. Hiram says that he swore an oath and cannot tell. After Colonel Burns tells Hiram that he will give him a pleasant surprise, Hiram almost tells him where Virgil is hiding. Eliza then says that her father dare not tell Burns, but, Hiram tells her to hold her tongue. Colonel Burns says that he will handle this, and says to Eliza that good girls are seen and not heard before patting her on the head. Eliza then holds her words, and walks away. Lisa says that can't be true, because Eliza was the only heroic ancestor of the Simpsons. Lisa goes back to the library and asks again if they have anything of Eliza Simpson, which they again say no, but she may try the film vault. Lisa finds a film of Eliza Simpson in 1952, at her 100th birthday. The man interviewing her claims she has had an extraordinary life, and asks if she had had any regrets. Eliza say that she has only one: that when she was a girl, she witnessed a great injustice, but she held her tongue and that the pat on her head by that wicked man has haunted her to this day.
Lisa is forlorn to discover that Virgil never was safely freed and he was a slave for the rest of his life, and that there are no noble Simpson ancestors. She then admits to Homer that she should have quit while she was ahead, instead of hearing the awful truth. After seeing how sad Lisa is, as well as being threatened by Homer to talk by changing the Thermostat, Grampa begrudgingly tells her the full story of Virgil and the Simpson family. He says that Mabel was on to Hiram, and that he would eventually tell Colonel Burns, so she cooked up some revenge. After opening the shed where Virgil was hiding, Hiram sees Mabel with a shotgun, saying to Colonel Burns that if she ever sees him on her property again, she will shoot him in the lower section. Burns then surrenders, and Mabel tells Hiram that she knew he would break the promise and that she is, by herself, taking Virgil to safety in Canada. Along the way they run into Abraham Lincoln who gives her his hat to disguise her hair. The longer they went, the closer they became, and when they crossed the Canadian border, Virgil proposed to Mabel, and she said yes. While in Canada, Mabel divorces Hiram and has a child with Virgil named Abraham (as a remembrance to Lincoln for what he did to help them), who is Abe's great grandfather, which shows that their part of the Simpson family is actually descended from Virgil, and not from Hiram.
Lisa then says the family regained their honor and they are 1/64 black. Lisa then asks Grampa why he kept this a secret, but he says that people from his generation are racist, and he didn't want to tell the story. Marge doesn't know what the big deal is, because nobody was bothered when they learned her father, Clancy, was French, which Homer says is the reason he loves drinking so much. Marge then tells him that she is French, not Homer, but Homer still thinks he is.
The episode was watched by 6.08 million households getting a 3.0/8 in the 18-49 Nielsen Rating, and was the second most-watched show on Fox that night, after a repeat of Family Guy and came second in its timeslot after The Olympics improving 15% from "Boy Meets Curl".