A banner reading 'SOMETHING ROTTEN!' hangs onstage as Tudor buildings are revealed on a Renaissance-era 1595 South London street ("Welcome To The Renaissance"). A Minstrel and Townspeople laud the societal advances being made, while a group of Puritans, including Brother Jeremiah and Portia, disapprove. The Minstrel explains that, unless you're superstar William Shakespeare, being a playwright is difficult ("Welcome To The Renaissance - Playoff").

Inside the theater, Nick Bottom rehearses with the Troupe, including Tom Snout, Robin, Peter Quince, and Nigel. Their patron, Lord Clapham, announces that Shakespeare has written a version of Richard II, the play the Troupe has been rehearsing, and demands they write a new play by the next day. Nick is frustrated ("Man, I Hate Shakespeare").

Back at home, Nick and Nigel are searching for a new idea when Shylock interrupts to collect Nick's debt. Shylock offers to become Nick's patron, but Nick refuses. Bea offers to get a job to help with expenses ("Right Hand Man"). Bea leaves to find work, Nigel tries to write, and Nick laments his situation ("Man, I Hate Shakespeare - Reprise"). Suddenly, Nick has an idea and heads to Soothsayer Alley, where Nostradamus tells him that the future of theater is… musicals ("A Musical; A Musical - Tag")!

Nigel and Portia meet and fall instantly in love, but Portia is unattainable as Brother Jeremiah's daughter. Nick tells Nigel about the musical and shares his first idea for a show: ("The Black Death"). Brother Jeremiah does not approve, and Lord Clapham ends his patronage, since Brother Jeremiah could jeopardize Lord Clapham's relationship with the Queen. Nick vows to solve the Troupe's money problem.

At the market, Nick and Nigel encounter Bea in disguise. She's gotten a job and is quickly called back to work by the Foreman. Nick leaves to find a new patron. In disguise, Portia enters and recites a verse of Nigel's poetry, impressed by his talent ("I Love The Way"). They are interrupted by a Messenger with an invitation from Shakespeare to attend a recitation in the park. Shylock offers Nick his services as patron yet again and reveals that Nigel is attending Shakespeare's recitation.

The crowd gathers for Shakespeare's dazzling recitation ("Will Power"). Shakespeare spots Nigel and Portia in the crowd ("Shakespeare's After Party 1"; "Shakespeare's After Party 2") and offers to read Nigel's poetry, but Nick accuses Shakespeare of stealing ideas. Brother Jeremiah takes Portia away, and Nigel goes after her. Nick finally agrees to take Shylock as a patron.

In Soothsayer Alley, Nick pays Nostradamus to look into the future for Shakespeare's greatest play: Omelette! Nick dreams of his new life as a famous playwright ("Nick Bottom's Gonna Be On Top").

Shakespeare finds out about Nick's plan from Eyepatch Man, and he vows to investigate.

The Troupe rehearses the musical ("It's Eggs"), and Shakespeare, disguised as Toby Belch, joins the production. Nigel sneaks off to visit Portia.

Nigel reads Portia the sonnet he's written for her. He is worried about approval from her father and his brother, but she encourages him to speak from his heart ("We See The Light"; "We See The Light - Playoff"). Unfortunately, Brother Jeremiah vows to lock Portia in a tower before sending her to Scotland. Taking Portia's advice, Nigel writes from his heart ("Nigel's Theme") and presents the new pages to the Troupe. They are very good, unlike Nick's musical, and Nigel tries to explain his inspiration ("To Thine Own Self Be True"). Nick and Nigel fight, Shakespeare takes Nigel's pages, and Shylock reveals that Omelette The Musical is sold out. Bea encourages Nigel to stick with Nick.

The Troupe performs the musical ("Something Rotten") with a hilarious jumble of musical theater references and a big production number ("Make An Omelette"), complete with EGGS. In the middle of the performance, Shakespeare reveals himself and tells everyone what Nick has done.

Nick is put on trial, where a Master Of The Justice will decide his fate. Bea arrives in disguise to act as Nick's lawyer and puts forth a plea of temporary insanity. Nick agrees and apologies ("To Thine Own Self - Reprise"). Then, Bea calls Shakespeare to the stand ("Shakespeare In Court 1)". Shakespeare convinces the Master of the Justice to banish Nick and Nigel rather than behead them ("Shakespeare In Court 2").

Nick, Nigel, Bea, and Portia leave England for the New World ("Welcome To America").