The evil Synonamess Botch, a maniacal ruler of the Murkworks, wants to foil Greenie's efforts and subject the Rushers to non-stop waking nightmares.
Meanwhile, two misfits – known as Ralph, the All-Purpose Animal (named so for his somewhat unreliable shapeshifting abilities), and Mumford, a Chaplinesque mime – are put on trial for their incompetence at work.
Botch deceives the three, claiming to be a friend of Greenie and telling them that Greensleeves can be saved if they go into Din and take the main spring from the Cosmic Clock.
A Fairy Godmother (FGM) twinkles in to tell Mumford and Ralph that they have been tricked and gives them three dimes to make a phone booth appear in case they need her help.
Ralph and Mumford find nightmare bombs scattered in an office, ready to be set off by Botch once it starts time again.
When they are finally freed from the nightmare, the Fairy Godmother transports them back to Frivoli, suggests that they give up after all their mistakes, and fires them from the hero business.
She tries to escape from his floating apartment in the sky and falls, landing on a mechanical serpent that attempts to stop Ralph and Mumford from reaching the Murkworks.
At the same time, Botch has his head vulture, Rudy, fly the spring back to Din as the final phase of his plan.
Botch retreats to a control room housing his master nightmare bomb button, "The Big Red One," with Ralph and Mumford chasing him.
In the form of a fly, Ralph tricks Botch into pressing The Big Red One, detonating all the nightmare bombs before Rudy can put the spring back in the Cosmic Clock, the still-immobilized Rushers being unaffected.
From the outset, director John Korty did not want to use the dialogue of the original script, but actor Marshall Efron thought his lines were perfect and played up the raunchier aspects of his character.
This new cut filled-out the remaining showings of Twice Upon a Time scheduled that month, prompting complaints of "censored" movies being shown on HBO.
This release contains John Korty's intended family-friendly cut, with some scenes roughly trimmed short to remove profanity that was still present.
It has also been shown early mornings on Turner Classic Movies, first on February 1, 2015 as part of the channel's TCM Underground block, and again on May 20, 2019.
The DVD contained both cuts, an audio commentary with John Korty and selected crew members (including Henry Selick), as well as the original theatrical trailer and TV spots.