The show opens with Cookie, alone and sweeping the floors in the diner where he works as the chef. He looks out of the window for approaching customers, but, as usual, there are none. Julie, the waitress, enters on roller skates – she thinks that a gimmick might boost business. Nina, the owner of the diner, enters, also lamenting the lack of customers. Rebecca, the upstairs tenant and the diner's only regular, enters. If they can't figure out a way to get more customers, they'll have to close the doors ("Throw Away the Key").

Just then, a customer appears! His name is Lucky, and he's not really a customer – he's looking for work. Tom, a genuine customer, then arrives. He is a third grade teacher and while getting ready for his first day of school this morning, he turned on "Schoolhouse Rock," and all of the characters suddenly jumped out of the TV and started singing his favorite songs from the show ("Rockin' Medley"). Nina interrupts his story: if they don't come up with a plan to save the diner before her sister comes home from a business trip in six hours, the diner will have to be shut down. Tom, thinking of his inspirational morning, wonders if a few songs might help cheer up Nina. She, however, is stuck on the thought of the six hours that she has left ("I Got Six").

Tom suggests that imagination inspires ideas, gesturing out to the audience and telling his friends that the audience members are ideas that have come to help save the diner. Julie says that she feels a spark of something beginning to happen ("Electricity"). Then, Rebecca suggests that the restaurant should have a zoo theme with live animals ("Four Legged Zoo"). The others reject this idea when they begin discussing who will take care of the animals, what the animals will eat and who will clean up a few hours after they eat ("The Body Machine").

Rebecca suggests another theme: a patriotic diner. They review the major dates and events leading to America's independence, which would be a part of that theme ("Fireworks"). Julie admits that it's a good idea, but says that it's a little overdone. Nina, in a panic, reminds the group that her sister will be there at nine o'clock, and they still haven't come up with anything ("Naughty Number Nine"). Lucky tells Nina not to worry, as he brings good luck ("Lucky Seven Sampson"). When he tries to leave, Nina convinces him to stay. He admits that he is having a good time and asks if they can guess his favorite "Schoolhouse Rock" song ("I'm Just a Bill"). Tom assures Nina that with everyone helping, finding a solution will be simple ("Elementary, My Dear").

Rebecca has another idea and runs up to her apartment. Nina admits that Lucky is good with numbers and tells him that if the diner ever turns around, she could use his help with the books. Rebecca returns with a ukulele and cowboy boots, since it is her dream to be a country singer. She thinks that the diner should be a trendy coffee shop with live entertainment, but she needs a guitar and doesn't have the money to buy one. Lucky tells her how she can make interest on her money by putting it in the bank, or how she can borrow money from the bank ("Dollars and Sense"). In the end, Rebecca still doesn't have enough to buy a new guitar. Julie offers the money that she makes from recycling old cans ("Energy Blues").

Cookie wonders who pays for recycling. Lucky and Tom explain that he does, through taxes ("Taxman Max"). Lucky then explains that the IRS is just a small part of the government, and Julie and the women describe the three branches of government against a circus backdrop ("Three Ring Government"). After the song, Rebecca enthusiastically suggests that the diner should have a circus theme; Nina wonders what goes on inside of Rebecca's head, which prompts an exploration of the human body ("Them Not So Dry Bones"). A fly buzzes past Nina. She tells the group that flies really get on her nerves, which cues a discussion of the nervous system ("Telegraph Lines").

With time passing quickly and only an hour until they pick up Nina's sister at the airport, they are desperate for a plan. They have reached the eleventh hour ("The Good Eleven"). Despite the trouble they are in, they are all having a good time together and have made new friends. The others say that they will support Nina, no matter what happens, and remind her that she has just as much of a say in the future of the diner as her sister, since Cleo is not the Queen of England ("No More Kings"). Inspired by the explanation of monarchy versus democracy, Nina is convinced that she can keep her diner. The group responds enthusiastically ("Interjections").

Cookie tells Nina that it's time to pick up Cleo. Nina looks around at her friends and at the diner... which suddenly gives her a new idea! She draws the group's attention to all of the colorful "stuff" that they've brought in while singing their favorite "Schoolhouse Rock" songs. They will have a "Schoolhouse Rock" restaurant and name it The Conjunction Junction Diner, because it's where they all come together. The group approves unanimously! ("Conjunction Junction / Finale").