After a long church dismissal, the Simpson family goes to the local supermarket for a Sunday brunch. The rule, according to Homer, is if there's a toothpick in it, it's free. While inspecting the freezer for ice cream, Homer has Lisa shoved inside to look for some different flavors. Marge has him pull her out and Lisa is shivering and possibly sick. On the way out, Homer spies the lobster tank and wants a lobster. However, he can't afford one. But then he gets the idea that if he buys a small lobster, he can fatten it up and then "eat the profits".
The next morning, while Homer is busy fattening up his lobster, Lisa is clearly ill and despite her claims otherwise, Marge insists that she stay home from school. She wants Lisa to take it easy on learning; one of Bart's video games will help soothe her nerves. The game Lisa first plays is a game called Dash Dingo. At first, Lisa is none-too-thrilled with the idea, but come the afternoon she can't put the game down. Just then, Ralph Wiggum pops up in her room; he is here to give Lisa her homework. Their class is reading The Wind in the Willows. After he leaves, Lisa continues playing the game.
Still hooked on the game and not having read the book, Lisa is able to deceive Marge into thinking she is still sick in order to stay home. Three days later, Lisa tries to get one more sick day, but at this point Marge is convinced that Lisa is merely feigning her illness. Despite Lisa's objections, Marge drops her daughter off at school. In class, Miss Hoover asks her if she got the reading assignment. She concurs, unfortunately, today the class is being tested on the book.
Working up the courage to face the test, Lisa tries to fluke her way through it but the fill-in-the-blank sentences render it to be impossible. Following a vision, Lisa is excused to the drinking fountain where she finds Bart in the hallway, with his shop class dummy in his place. Lisa explains that she is in danger of completely bombing her test when Bart agrees to take her into the boys' bathroom. Nelson buzzes them into the toilet stall, which is set up like an office cubicle and hands Lisa a cheat sheet. Lisa initially refuses the temptation to cheat, but seeing Groundskeeper Willie with his bare hand in a drain makes her reconsider. She winds up getting every last answer correct, including the extra credit question that was cut off by the copying machine.
Meanwhile, Homer's lobster is growing much bigger and soon it is too big for the fish tank. He throws it inside a kiddie wading pool, making it a free-range lobster. While feeding it, the lobster pulls Homer inside with it. Homer is angry with his entree, but seeing it cower makes him start to develop feelings for his lobster. When the lobster is large enough, Marge has a pot of water boiling and is ready to cook it, but Homer starts to see his lobster under a different light. He agrees to keep it as his new pet, calling it "Mr. Pinchy".
At the table, Homer is serving not lobster, but steamed cabbages. Bart is not happy with this change, but Homer explains that Pinchy is a member of the family and they won't be eating him. Marge takes this moment to announce she is proud of Lisa's newest achievement as she pulls out her test with an "A+++". Lisa is not happy with herself and runs up to her room.
At school, Nelson tries to sell Lisa the fraction test answers, but Lisa does not want to start cheating again. When she is called to Principal Skinner's office about the test, Nelson disavows helping her.
Principal Skinner tells Lisa that he is quite happy with her A+++; it has brought the school's GPA to its minimum standard and the school qualifies for a basic assistance grant. At this time, Lisa can't stand herself anymore and confesses to cheating on the test.
Despite the tainted achievement, Skinner and Superintendent Chalmers tell Lisa they may still get the grant money as long as they don't say anything. They take Lisa for a walk around the school, where they feel the grant money will do a lot of good for the students. Against her better judgment, Lisa agrees to keep quiet.
During the night, Springfield Elementary is ready for the grant money presentation. Comptroller Atkins awards Lisa the check, but Lisa reneges on her promise and confesses. The audience boos, but Atkins reprimands them; after all, surely they've all cheated at some time. The audience reconsiders and Homer and Marge carry her out of the room. It is revealed that the staff prepared for Lisa's honesty when Bart closes the door and locks it; and Comptroller Atkins is truthfully Otto in disguise. The school then welcomes the real Comptroller Atkins who presents a legal check. Afterwards, Superintendent Chalmers rushes him out the door while Principal Skinner tells the staff of a liquor store where they can cash the check.
At home, Lisa changes her A+++ into a big red "F", ending her plotline. But where is Pinchy? Homer tells Marge that Pinchy got himself dirty in the yard and he had put him in a hot bath. But when Bart asks about a delicious aroma that he smells, Homer learns it is the smell of lobster, and is worried that he has cooked Pinchy's goose. He bolts out of the room.
That night, at the table, Homer is crying while he eating Pinchy's dead body. When asked if he will eat the whole thing alone, Homer confirms, saying Pinchy would've wanted it this way.