Act One

At Arch Systems, a technology company in 1971, high schooler, Michael Dork, is mopping the corridors outside Arch's computer room. Once the coast is clear, Michael sneaks his way into the computer room. Surrounded by towers of spinning reels and "state of the art" equipment, he communicates with his best friends and accomplice, Lucas Lloyd, who brings him an Accessible Memory Storage device onto which Michael begins to transfer the work he's done to develop a digital language that would allow computers to communicate with each other... but an alarm is sounded! Lucas and Michael hit the ground running in a daring escape while thinking of the incredible technological advances existing all around them ("Living in the Future Now"). Elaine Friend & Samantha Powden and Huey Phillips & Wayne Pagoda, the popular kids' sidekicks, chime in, espousing their love of television and telephones.

The next day, Michael and Lucas (along with their friends, Marvin Camden and Francis Wier) are welcoming the delivery of two brand new ASR 33 teletype computers to their school. Marvin and Francis are a bit more excited by the delivery of their new Star Trek action figures and the imposing Starship taking shape in the back of the computer lab that they've made from cardboard boxes. This, they believe, will take first place at the annual Sci-Fi Competition and give them the chance to meet the entire Starship Enterprise Crew... especially Uhura. The boys exchange friendly jabs at Michael about their classmate and seeming-heir to Arch Systems, Eddie Arch. Michael responds by explaining the worth of enduring Michael's torture: the opportunity to create his computer communication code. But, as Michael plugs the hard drive into the new computer, all of his work is deleted. Whether it's Francis' daily-donned Cub Scout Patches, Lucas' obsession with writing a sci-fi novel or all of the boys' general inability to talk to girls, they rally together and promise they'll always look out for one another ("Don't Let 'Em Bring You Down"). Elsewhere, a beautiful girl named Holly Manson is packing up her belongings while taking off her make-up to put on glasses ("Little Things – Prereprise"). Holly is excited about being able to come into her identity as a proud and fully realized feminist with aspirations of being the first female astronaut, a chance that she's yet to have because she's cursed with both brains and looks ("Brains and Looks"). Now, though, Holly has decided that she needs to be less attractive to be taken seriously. In the school locker room, Eddie, with the assurance of Wayne and Huey, thinks the opposite of himself. His girlfriend, Leia Dawkins, accompanied by Samantha and Elaine, feels the same. She has plans for her and Eddie's future that will certainly all come true because she and he are such breathtakingly beautiful humans. All of the navel gazing is interrupted by the school's Principal, who calls Michael into his office and bans him from the computer lab because of Michael's "theft" from Arch Systems.

Later, reeking of devastation, Michael joins his schoolmates in a class while Lucas is being questioned by Ivanka and Marina, the Yugoslavian exchange students, who have yet to master English. The Principal enters and introduces new student, Holly. Her geeky appearance elicits a cavalcade of typical teenage ribbings from her new classmates. Holly's situation is made even more difficult when she proclaims ambitions to be an astronaut and announces her love of computers. Michael's ears immediately perk up, realizing she may be his way to continue his computer work despite being banned from the lab. He's quickly attacked and viciously described by his classmates ("Slacker"). This doesn't slow down Michael's mission. He and Lucas track down Holly and, in an uncomfortably adolescent exchange, propose the plan to her. She agrees! They exit and are replaced by Samantha, who confesses her nerdy side ("Brains and Looks – Reprise").

Three weeks later, the Starship is coming along quite nicely while Holly and Michael's progress seems to be crawling. Adding insult to industry, Arch Systems has proclaimed a great breakthrough in their computer communication network coding. Holly and Lucas are alone inside the computer lab, with Michael looking on. In the privacy of their minds, he and Lucas admit their feelings for Holly as Francis and Marvin peep on the girls' gym class and, to the accompaniment of Leia's praises, Eddie goes before his father to hear what part of the business he will be in charge of after high school graduation ("Little Things"). It's resolved that Michael will ask Holly out, with the support and help of his friends ("Don't Let 'Em Bring You Down – Reprise"). When Eddie explains that his father isn't giving him a department, but rather shipping him off to a military academy, Leia is appalled and storms off, leaving him to contemplate his future ("Slacker – Reprise").

At The Planetarium, where he works, with an in-ear monitor connected to the CB radio being manned by Lucas, Marvin, and Francis, a nervous Michael meets Holly. After a very ineffective attempt to deliver the cheesy lines he's being prompted, Michael abandons the in-ear monitor and speaks from the heart. In a breathtakingly romantic gesture, he illuminates the stars of Planetarium ("We're Not Alone"). Meanwhile, Eddie, in need of a way to impress his father and inherit a portion of the Arch System, talks with Huey and Wayne. Wayne then produces photos of Holly in her previous un-nerdy garb and concocts a plan. The act draws to a close with all the kids imagining the various ways they're going to change their lives ("Ticket Outta Loserville").

Act Two

The Sci-FI Convention is underway, as evidenced by the abundance of nerds filling the stage ("We're Not Alone – An Uptempo Reprise"). Marvin and Francis take second in the Starship of the Future competition because a wearable Flying Saucer masterpiece made by Samantha is awarded first place. Francis and a smitten Marvin congratulate her and are joined by Marina and Ivanka, who promise to throw Samantha a party after they study English, a task with which an eager Francis offers his assistance.

Later, in the computer lab, an overworked and yet-to-be successful Michael and Holly deny Marvin and Lucas' suggestions to bowl. Having been stood up by the two before, Lucas angrily exits. Upon further consideration, Michael and Holly decide that they have been working too hard. They lock their disks in a safe and leave the lab to take a break. Lucas sees them from afar as his frustration and jealousy reaches its boiling point ("Holly, I'm the One"). As if on cue, Eddie approaches with his goons and makes a proposal to Lucas. Eddie will present the publishing portion of Arch Systems with Lucas' book if Lucas will steal Holly and Michael's disks for him. Lucas agrees.

Holly catches the boys as they're stealing the disks. To counter, they make it clear to her that they have photo evidence of her former persona, threatening to expose her past to NASA and any credible establishment to which she might apply, Eddie blackmails her into working with him and abandoning Michael. Holly considers her predicament and, after writing a note to Michael, decides to give in to Eddie's demands ("Long Run"). Meanwhile, the kids at the party at Ivanka and Marina's celebration for Samantha's win question their own status in life ("What's So Weird about Me?") Michael enters, searching for Holly since he was unable to find her at her house, while Samantha explains her nerdiness to Elaine and Leia. When Michael catches a glimpse of Holly across the party, he advances but is blocked by math genius, Susie, who distracts him while Holly makes an escape and runs into Eddie. Eddie explains that the only way to be sure she is reliable in their deal is to seal it with kiss. Unbeknownst to Holly, Michael witnesses their embrace. He confronts them for a moment before being brushed off by Eddie and left alone ("Holly, I'm the One – Reprise").

Holly has been working tirelessly for Eddie, but hasn't made the level of advancements he expects. He chastises her and leaves a frustrated Holly by herself to contemplate the extent of her hatred for him ("Sick"). After finding out that Eddie hadn't followed through with his end of their bargain, Lucas has a series of disdainful thoughts of his own, as does Leia. Lucas confesses his part in the plot to Michael, who is rightfully upset by the news. A few days later, Holly and Eddie can be found in the same positions: Holly is working intensely and Eddie is doing nothing but berating her. Holly has a stroke of genius that may be the missing piece in the puzzle. Elated, Eddie calls a press conference for the following morning. On the phone, Lucas is being informed and taking down notes from Holly. He rushes to Michael and reads the letter that Holly wrote when she agreed to help Eddie. It explains her dire circumstances. Lucas then shares with Michael the missing piece that Holly discovered: an address. The code that she and Michael had been writing wasn't pinpointing the location of the machine to which the message was being sent. They needed to input the exact address of the receiving computer. Through Lucas, Holly has suggested that Michael send a message two minutes before Eddie's demonstration message is sent in front of the press, thus making Michael – not Eddie and Arch Systems – the first person to send a message from one computer to another successfully. Their plan is in motion ("Genius").

Their plan goes off without a hitch! The first message sent from one computer to another says "I guess it really pays to be a slacker. Michael Dork." With Eddie's devious plot foiled, his father storms out of the room, and Eddie chases after him, begging for forgiveness. Holly then sends Michael a response: "I love you, Michael Dork." Later, Holly finds Michael at The Planetarium, and they reconcile, topping it off with a kiss ("We're Not Alone – Reprise").

All of the students gather in the computer lab. Leia approaches Lucas and tells him how much she loved his book; especially the little characters, OB One Cannoli and R2 Me 2, but explains that she thinks it is better-suited to be a movie than a book. Lucas confesses to having always thought of Leia as a princess of sorts, and a new bond is formed. Holly and Michael are welcomed by cheers as they enter, carrying the latest copy of Computer World magazine. The first page story is about them: "Beauty and the Geek – Change the World." The room erupts in celebration and cheer as the curtain falls ("I Don't Wanna – Ticket Outta Loserville").