Stilled trapped in the time of the Three Musketeers, Rebecca is mistaken for Madame D'Urfe, an assassin hired to kill King Louis XIII. Jules and Phileas must persuade the Three Musketeers to reunite to rescue Rebecca, and save the King by defeating Richelieu. Of the Musketeers, Athos is dead and the other two are relucant, but are swayed to join. Porthos is a dead-ringer for Dumas in the 19th century. Adding further confusion, Richelieu is a twin for Fogg, Louis XIII for Jules, and D'Urfe for Rebecca. Apparently they have not just traveled in time, but into a parallel dimension of some sort. Rebecca plays along with the Cardinal, who is forced to kill the real Madame D'Urfe when she shows up so as to cover his tracks. Meanwhile, Passepartout works to discover the secret to the Phoenix to return all to their rightful place and time, aided by his own counterpart, a scientific genius. Rebecca fails to kill the King, and Richelieu hauls her away, then tries to have the King killed. Fogg, Jules, and the Musketeers break into the prison and a fight ensues. They rescue Louis, but Passepartout arrives, freezing time for everyone except his friends, who escape back to the 19th century. In the "present", they have the code. Fogg confronts the assassin Cavois, and they have a duel of "Russian Roulette" which Fogg wins.

The adventure begins. In Paris, Jules Verne, a student with the ambition of becoming a great novelist and playwright, unwittingly attracts the attentions of the League of Darkness and its leader, Count Gregory, with his visions of fantastic machines and ideas for the future. The League, hoping to use Jules' ideas for their own nefarious purposes, kidnaps Verne and tries to steal the images directly from his imagination. He is saved by British secret agent Rebecca Fogg who had been sent to Paris to find the very machine being used to extract the images from Jules. Meanwhile in London, Rebecca's distant cousin, former secret agent Phileas Fogg, has embarked on a life of gambling after the death of his father, Sir Boniface Fogg, former head of the British Secret Service. Unaware of the greater plan, Phileas "wins" the airship Aurora and her navigator, Passepartout, during a game of cards.

Rebecca has a friend of hers trying to decipher a secret code, behind the back of her superior. She is threatened with a scorpion in her bed, which she manages to kill. Phileas offers to help, but the codebreaker is killed under his protection by the mysterious Cavois. Cavois makes another attempt on Rebecca's life, which is thwarted by a bulletproof corset. Phileas tries to confront Cavois but is thwarted: Cavois leaves him for later. Meanwhile, Jules is meeting with his old friend Alexandre Dumas. It turns out he was a spy at one time, and created the code and hid the transcription code in his novel The Three Musketeers. Dumas is up to his ears in debt, in part because he is trying to build a machine, the Phoenix, based on designs by Cardinal Richelieu from 200 years earlier. The others meet up with Jules, and are forced to flee before Dumas' debtors. Passepartout inadvertently activates the time machine, and the four go back 200 years. As they step out to investigate, Passepartout inadvertently activates the time machine again, leaving the other three stranded. Worse, Rebecca is mistaken for an assassin and taken before Richelieu, who wants her to kill the king...

Traveling to Paris to celebrate Jules' birthday, Phileas, a disabled Rebecca, and Passepartout, along with Sir Hugo Bezel (chief architect of Paris), arrive just as a golem is on a murderous rampage through the city. After Jules is arrested for the crimes, Phileas and Rebecca each go about in their own way to discover the true murderer; Phileas by seducing the beautiful and talented Angelique, and Rebecca by dispatching Passepartout to do research. It is Jules, however, who unmasks the culprit.

A sarcophagus containing the remains of Nepka, an Egyptian high priest, is being transported to New York by Phileas Fogg for his old schoolmate, Professor Alexander Douglas, and an unusual woman, Adriana Locke. It becomes clear that Phileas has fallen under the spell of Adriana when he shows no interest in the mysterious deaths surrounding the sarcophagus. Jules, Rebecca, and Passepartout investigate, discover Adriana's evil intent, and defeat her purely.

Using an idea stolen from Jules Verne (from In the Beginning), the League of Darkness construct a giant underground tunneling machine, the "Mole." The League first kills a diplomat to get papers giving their own agent access to Queen Victoria, whom they plan to kill. While Rebecca goes to investigate the sewers where the Mole is, Phileas first believes that Jules was involved since one of his drawings was found in connection with the Mole. After a bit of slapping around, he eventually believes Jules and recruits him to help track down the Mole. Jules creates a series of tracking devices, but is then kidnapped by the Mole's female commander. They still want him to assist them, and torture him when he doesn't. Rebecca has figured out who the League's agent is at the Queen's meeting, and goes after him with the tracking device the League uses to guide the Mole to its victims. The agent is skewered on the Mole's bore, and with the aid of a giant magnet created by Passepartout, Phileas pulls up the Mole and punches out the Commander. Jules gets the gratitude of the Queen and the four decided to stay together.

The League of Darkness executes an elaborate plan to kidnap Phileas and brainwash him into assassinating Queen Victoria.

Hoping to shift the balance of power in the United States' Civil War, the League of Darkness heads across the Atlantic in the Prometheus while being pursued by the crew of the Aurora. When the Aurora crashes, Phileas, Rebecca, Jules, and Passepartout are welcomed into the home of a true Southern belle, Saratoga Browne, with whom Phileas falls in love. Passepartout and Rebecca join forces with the Union to try and defeat the Prometheus, while Phileas and Jules go after the airship when Count Gregory kidnaps Saratoga to force Phileas' hand. Jules manages to distract the airship's crew while Phileas rescues Saratoga. Count Gregory uses the power of the ship to reassemble his component parts into an indestructible cyborg, but a gunshot from the Union cannons knocks him out. Phileas and Saratoga escape by parachute, but a final gunshot from Gregory kills Saratoga just as Phileas proposes marriage to her. The Prometheus is brought down, leaving a despondent Phileas.

Phileas Fogg comes into possession of a single black glove covered with Cabalistic symbols. The glove, it turns out, is being hunted by two men: a mysterious Cabalistic sorcerer named Vargas, and a Chinese mystic, Zai Chao. Vargas confronts Fogg, threatening Passepartout's life for the glove. Fogg, though, manages to defeat Vargas despite his mystical abilities. Meanwhile, Rebecca has been kidnapped by Zai Chao, and is being used as a hostage to force Fogg to give him the glove. In the final confrontation, Fogg and the others square off against Zai Chao's martial arts fighters. Zai Chao manages to get the glove, but Rebecca shoots him, causing the glove's energy to run wild and reduce Zai Chao's body to a pile of dust and his spirit to a shadow.

The group is summoned to British Columbia after an American General, Steele, is kidnapped by Indians from the British territory. To avoid a war between the two countries, Fogg and the others must find Steele. They discover that Steele's kidnapping was engineered by Count Gregory and the League of Darkness. The League steals the Aurora and drops Steele's corpse off at West Point to further set the two countries upon each other. With the aid of a local Indian, the team finds Gregory's waterfall hideout, from which he plans to launch a rocket and destroy West Point as President Lincoln gives a speech. Despite Phileas' reluctance to engage Gregory (since the Count killed his beloved in the episode "Southern Comfort"), Rebecca enters the hideout only to be captured. She is tied to the rocket and launched. She manages to escape and redirect the rocket, while Fogg and Verne break free of Gregory and knock him back into the waterfall where he plunges to his seeming death.

While waiting for Passepartout to arrive from Baltimore with the Aurora, Jules, Rebecca, and Phileas pass the time aboard the gambling boat, the Memphis Belle; Phileas by gambling and Jules and Rebecca by socializing with a newspaperman, Sam Clemens. They meet up, also, with a group of ex-Confederate soldiers, including Frank and Jesse James, bent on a life of crime who steal the Aurora and kidnap Passepartout. Using alcohol and a fantastic story about "Steeley Joe", Passepartout is able to escape from the gang and find refuge in the town of Apache Wells. Meanwhile, Jules, Rebecca, Phileas, and Sam Clemens also arrive in Apache Wells and with the help of the local saloonkeeper, Miss Lily, and their own version of "Steeley Joe," they are able to thwart the menacing group of bandits and return Apache Wells to a peaceable town.

The evil spirit of a dead mad anarchist, Lazarus, takes possession of Passepartout at a seance for Passepartout's recently-deceased Aunt Louisa. Lazarus, who died at the hands of Phileas, is intent on returning the favor. When Passepartout is thought mad and committed to an asylum, the spirit of Lazarus passes to Rebecca. With the help of the spirit of Aunt Louisa, Lazarus is banished before his evil plan is accomplished.

On assignment to find invasion plans, Rebecca escapes empty-handed from the castle of Prussian General von Kessler, with the aid of the Aurora and her cousin Phileas. They are then summoned back to Fogg Manor, Shillingsworth Magna, with the news that the body of Phileas's father has disappeared from the family crypt. The group travels to the manor, where a number of strange occurrences have been reported. The vicar has called in an exorcist, who seems smitten with Rebeccas' charms. Phileas, who left the Secret Service after his father's actions got his brother killed, is none too pleased or interested in the whole affair. Passepartout eventually discovers that Boniface's body wasn't stolen, but that the bones were reduced to dust by an electrical storm that triggered a discharge. The same discharge reanimated the skeleton that was in the crypt, that was brought back from the Crusades by Boniface's ancestor. The vicar believes the bones are those of an angel, but Jules believes they are of an alien. Meanwhile, von Kessler and his men are tracking Rebecca, who unknowingly has the plans after all. Jules, Phileas, and Rebecca are trapped in the church by von Kessler when the alien is reanimated. Fortunately it is friendly, and departs in a spaceship. The ship destroys the church, which provides enough of a distraction for the group to capture von Kessler. At the end, Phileas reconciles with his father's actions in life and lets Passepartout build a memorial fountain over the dusty remains of Boniface Fogg.

On the death of Professor Maréchal, his daughter persuades Jules and Phileas to take his remains to the coast, where they find the machine Maréchal created that can supposedly bring the dead back to life. The daughter sends the men away and then tries to revive her father. The attempt succeeds, but she finds out that her father was working with the League of Darkness, and he killed himself to prevent the finished device from falling into Count Gregory's hands. Phileas and Julies return and manage to disrupt the scheme, and Maréchal dies one final time.

When Jules contracts yellow fever in Tangiers, a famous doctor takes him for treatment to a Corsican hospital that is secretly controlled by the League of Darkness.

When Rebecca investigates the murder of a British envoy in London, she must go undercover as an actress to attract Angelo Rimini, Duke of Carpathia and the prime suspect. He becomes infatuated with her and seemingly vice versa, and spirits her off to Carpathia. Phileas is none to thrilled with the Secret Service endangering her and pursues. The three of them evade vampires and Phileas and Jules make it to the castle and see Rebecca falling under Rimini's sway. Meanwhile, vampires take the Aurora and Passepartout fakes his death. Rebecca learns of Rimini's plan to take over the world with an army of rocket-powered vampires. She teams up with the others and manage to sabotage the jetpacks. As Rimini looks on, a regretful Rebecca departs with the others as his vampire army crashes and burns.

While investiging a country priest's murder, Jules is lured to a secret base of the League of Darkness, where they are creating a flying ship called the Prometheus. Jules accepts a commission at the behest of the ship's beautiful commander, unaware of the League's true purpose. The others come to investigate, and the Aurora is taken captive. Rebecca discovers that the League plans to use both ships to help the Confederacy win the Civil War. While Phileas confronts the League's leader, the centuries-old "cybernetic" Count Gregory, Jules turns against the League. Phileas and Passepartout recover the Aurora, while Jules is forced to choose between the commander and Rebecca. He goes with Rebecca, and the two manage to escape. The episode ends with the Aurora giving chase to the Prometheus as it heads west to the United States.

Following the death of Saratoga Browne, Jules, Rebecca, and Passepartout have their hands full with a suicidal Phileas. Packing up the Aurora, they decide to go on a tour of the United States. They meet up with a young boy, Al, who they find is mechanically inclined and partially deaf. They also discover he is an incredible mechanical genius, having recreated the design of the Cardinal's Chariot (from "The Cardinal's Design). It lacks time-travel capability, but the miniature armored model can hover and move. Phileas' current gambling partner, an arms dealer, finds out about Al and his invention, and decides to finance it with the help of the Union. The others browbeat Phileas into financing a hearing operation for Al - they go to find the boy and find out about the creation of the new tank. Concerned that it will disrupt the balance of power between the Union and the Confederacy, the group resolves to stop it. They manage to rescue Al and destroy the hover-tank. At the end, they pay for Al's operation. As they head west, they find that Al's full name is Thomas Alva Edison.

When a college friend of Rebecca's, Amateratsu, and her grandfather Kajimori travel to Paris, the grandfather is kidnapped by the Inquisitor, a member of the League of Darkness. Kajimori has knowledge of a potion of "enlightenment," which he has passed on to Amateratsu. Amateratsu and Jules have become involved, and the League go after her when Kajimori tells them nothing. Rebecca and Phileas become involved when the two are kidnapped. Amateratsu gives her grandfather the potion, and he uses it to destroy the Inquisitor by showing him the "light" before himself disappearing.

A ship carrying the Spanish Ambassador Senior Sel Fuego and his mysterious cargo runs aground in the Sargasso Sea, and Fuego seems to disappear into a mirror. While Verne is plagued by strange visions, the Foggs and Passepartout go to investigate, and the Foggs pass through a dimensional curtain. They are imprisoned, and find out that Count Gregory and the League of Darkness are behind the sceheme. By entering the other dimension, Phileas and Rebecca caused the creation of "Similars" back in the real world. Working together with the "Similar" of Fuego (who is also a prisoner), the three duplicates plan to kill Queen Victoria. Verne realizes his "friends" are imposters and convinces Sir Chatsworth. The two of them fail to convince the Queen, however. The real Phileas asks that Rebecca kill him, as this will destroy his own Similar. Apparently the Holy Grail, Fuego's cargo, recognizes his willingness to sacrifice himself and frees them. With the aid of Passepartout, who has been trapped aboard the Aurora within the magnetic field, they return to the real world, which destroys their Similars.

While traveling over Montravia, the Aurora crashes and the local constabulary mistakes Passepartout for King Carl V, for whom he is a dead ringer. Carl is a lackabout, and they need a king who will go through the proper actions and sign a treaty. Passepartout agrees, with Phileas and Jules playing the role of his valets. Meanwhile, Rebecca tracks down the true king and imparts a few important lessons. Meanwhile, Lord Tyrol is working with the King's fiance to take the throne for himself. When Jules reveals the deception to her, she informs Tyrol and he attacks. Carl and Passepartout team up to take down Tyrol together.

While Jules tries to help Count Kugarin launch a rocket to the moon, Phileas gambles everything he owns against the Russian in a series of contests.