At a New Millennium Eve party Blackadder and Baldrick test their new time machine and ping pong through history encountering famous characters and changing events rather alarmingly....
The film opens at Blackadder Hall where the present day Lord Blackadder (Rowan Atkinson) is entertaining guests on New Year's Eve, 1999. As a scam, Blackadder informs them he has invented a working time machine and wagers £30,000 that he can bring back anything they ask for. His guests – Archbishop Melchett (Stephen Fry), Archdeacon Kevin Darling (Tim McInnerny), Lieutenant George (Hugh Laurie) and Lady Elizabeth (Miranda Richardson) – announce that, if Blackadder is to win, he must bring back a Roman centurion's helmet, the Duke of Wellington's boots, and a really smelly pair of 200 year old underpants. Blackadder intends to scam his guests by dredging the items from his personal store. However, he is stunned to discover that the time machine, built by Baldrick (Tony Robinson) after plans by Leonardo Da Vinci, actually works.
The pair first land in the Cretaceous Period, where they are attacked by a massive Tyrannosaurus. Baldrick uses his underpants to beat back the dinosaur, who takes one sniff and falls over dead. Lord Blackadder muses, "Fascinating. One of history's great mysteries solved. The dinosaurs were, in fact, wiped out by your underpants." When attempting to reset the dials to return to the present, Baldrick reveals that this is impossible, as he never got round to writing the dates on them.
After configuring the dials on instinct, Blackadder and Baldrick land back at Blackadder Hall at the court of Queen Elizabeth I, with Nursie (Patsy Byrne) and Lord Melchett at her side. The Queen, mistaking him for his ancestor, Lord Blackadder, decides to behead him, unless he has a gift for her. Blackadder first offers a supermarket loyalty card, upon which the Queen screams, "Kill him!" He then offers her a Polo mint, which the Queen proclaims to be "the tastiest thing in the history of the world". She rewards him with her crown, then orders him away to bring back more breath mints on pain of having his head smashed in.
On his way back to the machine, Blackadder literally runs into William Shakespeare (Colin Firth). After receiving the Bard's autograph, Blackadder punches him in the face, remarking, "That is for every schoolboy and schoolgirl for the next four hundred years!" Blackadder tells Shakespeare that his plays, which will cause untold suffering for untold generations of youths, are nothing but people "in stupid tights... talking total crap," then kicks him in vengeance for Kenneth Branagh's four-hour Hamlet film. Stunned, Shakespeare asks, "Who's Ken Branagh?" Blackadder smugly retorts, "I'll tell him you said that, and I think he'll be very hurt!"
Then, Blackadder returns to the machine and tries very hard to remember how the dials were set. He then sets the dials and is happy until the time machine materializes into a space battle. Blackadder quickly realizes that they may have gone too far and resets the dials again. After that, Blackadder and Baldrick land in Sherwood Forest and are captured by Robin Hood (Rik Mayall). However, Robin is horrified when Blackadder begins rattling off the flaws with his lifestyle. Blackadder smugly reminds the Merry Men that they face certain death if they're caught, live in total squalor with no toilet, yet give all they steal to the poor, who do nothing but "sit on their backsides," waiting for the next cash instalment. Enraged, the Merry Men promptly shoot Robin full of arrows. Then Maid Marian (Kate Moss), smitten by the "gorgeous" Blackadder, proceeds to have sex with him. Before leaving, Blackadder takes Robin's hat as a trophy.
A further attempt to reconfigure the dials results in the time machine landing at the Battle of Waterloo and squashing the Duke of Wellington (Fry) just before the fighting begins. Blackadder steps out of the machine only long enough to steal the Duke's boots to win his bet.
One last attempt to set the dials aright lands them at Hadrian's Wall in Roman Britain. Intriguingly, the wall is being guarded by Blackadder's centurion ancestor, with a Roman-era Baldrick as his shield-carrier. After stealing his ancestor's helmet, Blackadder and Baldrick escape just ahead of a charging wall of Braveheart-style Scotsmen wearing blue face paint.
Back in the time machine, Blackadder is becoming more discouraged about ever going home, but Baldrick comes up with "a cunning plan". Baldrick mentions that dying men have their lives flash before their eyes and that, if Blackadder was about to drown, he might remember how the dials were originally set. Blackadder agrees with this, but instead almost drowns Baldrick in the time machine toilet. As Baldrick's life flashes before his eyes, he remembers how to set the dials to return home.
Back in 1999, the party guests are very impressed by his trophies, but due to Blackadder's interference with history, Robin Hood is completely unheard of, William Shakespeare stopped writing plays and is instead credited as the inventor of the ballpoint pen, and Britain has been ruled by the French for two hundred years following Napoleon Bonaparte's victory at Waterloo. Horrified by the sight of a traditional garlic pudding and Archdeacon Darling wearing a tutu and ballet slippers, Blackadder leaps back into the time machine, screaming, "We've got to save Britain!"
This is accomplished by encouraging Shakespeare, flattering Robin Hood, and preventing the death of the Duke of Wellington. They then return home to collect Blackadder's winnings from the amazed partygoers. After Melchett comments what damage an unscrupulous person could do with a time machine, Blackadder perks up. He tells his friends to go upstairs and watch the New Year's festivities on television, assuring them he'll soon return.
The four guests sit down to watch the broadcast of the royals and the prime minister arriving at the Millennium Dome. Blackadder – now the absolute monarch King Edmund III – steps from a limousine and is joined by Prime Minister Baldrick. The King is married to the beautiful Marian of Sherwood (Kate Moss). BBC correspondent Jennie Bond gushes about the King's 98% approval ratings, the success of Baldrick's cabinet, and the abolition of Parliament. The film ends with the Blackadders having finally triumphed, with their descendant having become the ruler of Britain and millennia from now, the ruler of the entire universe.