The film begins in an unnamed and war-torn European city in the late 17th century (dubbed "The Age of Reason" in an opening caption), where, amidst explosions and gunfire from a large Turkish army outside the city gates, a fanciful touring stage production of Baron Munchausen's life and adventures is taking place. Backstage, city official "The Right Ordinary Horatio Jackson" (Jonathan Pryce) reinforces the city's commitment to reason (here meaning uniformity and unexceptionality) by ordering the execution of a soldier who had just accomplished a near-superhuman feat of bravery (Sting in a cameo), claiming that his bravery is demoralizing to other soldiers. Not far into the play, an elderly man claiming to be the real Baron interrupts the show, protesting its many inaccuracies. Over the complaints of the audience, the theater company and Jackson, the "real" Baron gains the house's attention and narrates through flashback an account of one of his adventures, of a life-or-death wager with the Grand Turk, where the younger Baron's life is saved only by his amazing luck plus the assistance of his remarkable associates: Berthold (Eric Idle), the world's fastest runner; Adolphus (Charles McKeown), a gunman with superhuman eyesight; Gustavus (Jack Purvis), who possesses extraordinary hearing, and sufficient lung power to knock down an army by exhaling; and Albrecht (Winston Dennis), a fantastically strong man.
When gunfire disrupts the elderly Baron's story, the importance of saving the city eclipses the show. The Baron wanders backstage intending to die, until the exuberantly enthusiastic questioning of Sally Salt (Sarah Polley), the young daughter of the theater company's leader, convinces him to remain living.
Insisting that he alone can save the city, the Baron escapes the city's walls in a hot air balloon constructed of women's underwear, accompanied by Sally as a stowaway. The balloon expedition proceeds to the Moon, where the Baron, rejuvenated the adventure of escaping to the moon, finds his old associate Berthold, but angers the King of the Moon (Robin Williams), who resents the Baron for his romantic past with the Queen of the Moon (Valentina Cortese). A bungled escape from the Moon brings the trio back to (and beneath) the Earth, where the Roman God Vulcan (Oliver Reed) hosts his guests with courtesy and Albrecht is found. The Baron and Vulcan's wife, the Goddess Venus (Uma Thurman), attempt a romantic interlude by waltzing in air, but this cuts short the hospitality and Vulcan expels the now-foursome from his kingdom into the South Seas.
Swallowed by an enormous sea creature, the travelers locate Gustavus, Adolphus, and the Baron's trusty horse Bucephalus. The Baron (who again appears elderly after being "expelled from a state of bliss," in his words) struggles with the conflicting goals of heroism and a peaceful death, before deciding to escape by blowing "a modicum of snuff" out into the sea creature's cavernous interior, which causes the sea creature to "sneeze" the heroes out through its whale-like blowhole.
Back ashore, the Turkish army is located but the Baron's associates are now too elderly and tired to fight the Turk as in the old days. The Baron lectures them firmly but to no avail, and he storms off intending to surrender to the Turk and to Jackson; his cohorts rally to save both the Baron and the city.
During the city's celebratory parade, the Baron is shot dead by Jackson. An emotional public funeral takes place, but the denouement reveals that this is merely the final scene of yet another story the Baron is telling to the same theater-goers who were attending the theater in the beginning of the film. The Baron calls the foregoing "only one of the many occasions on which I met my death" and closes his tale by saying "everyone who had a talent for it lived happily ever after."
An ambiguous finale reveals that the city has indeed been saved, even though the events of the battle apparently occurred in a story rather than the film's reality. The Baron rides off on Bucephalus. As the Baron and Bucephalus are bathed in the light of the sun parting through the clouds, they apparently disappear, and the credits roll over a triumphant blast of music.
The stories were also made into films in 1911 (Les Aventures du baron de Münchhausen), 1943 (Münchhausen, script by Erich Kästner) and 1961 (Baron Prášil). His most famous adventures are referenced in a 1979 movie Tot samyi Münchhausen by Russian director Mark Zakharov which depicts Baron Münchhausen as a tragic character, struggling with conformity and hypocrisy of the world around him. Gilliam's film has many visual similarities to the 1943 version and the production company was legally obliged to add a disclaimer to the film's posters and closing titles to the effect that Gilliam's Munchausen was an original movie unconnected to the earlier version.
Young star Sarah Polley, who was nine years old at the time of filming, has described it as a traumatic experience for her. "[I]t definitely left me with a few scars ... It was just so dangerous. There were so many explosions going off so close to me, which is traumatic for a kid whether it's dangerous or not. Being in freezing cold water for long periods of time and working endless hours. It was physically grueling and unsafe.
Gilliam was left somewhat embittered by the experience and in interviews has often used Munchausen as a shorthand for a fiasco. However, in a commentary track on the DVD edition of Tideland, Gilliam now says that Munchausen is one of the films that his fans most often cite as a favorite. Gilliam noted the irony of the situation, adding that an artist can never really tell what work they produce will actually endure.