Following his capture by the Time Lords, the Doctor is brought before their High Court, charged with stealing a TARDIS and interfering in the affairs of other species, and sentenced to death. While he awaits his execution, however, three Time Lords on a sub-committee to monitor the work of the Temporal Scanning Service detect temporal interference on the planet Earth. Since the matter clearly needs handling but the Time Lords cannot be seen to act, Sardon -- an agent of the Celestial Intervention Agency -- suggests to Ragnar and Milvo that they send an agent with deniability, whom they can plausibly claim was acting on his own. Sardon thus approaches the Doctor with a proposition: if the Doctor carries out this mission for the CIA, his death sentence will be commuted to a period of exile. The Doctor agrees, on condition that he first be allowed to see for himself that the soldiers kidnapped to fight alien war games have been returned to their proper places in time and space.

On 18th-century Earth, Major-General Sir Arthur Wellesley, the future Duke of Wellington, nearly suffers a fatal accident aboard the HMS Trident while returning from a successful campaign in India. Fortunately, someone shouts a warning to Wellesley, who narrowly avoids being brained by a falling main’sl block -- which appears to have come out of nowhere. Wellesley has nearly become a victim of the game between the Players, who live outside the boundaries of time and space and treat history as their plaything. This attempt to remove Wellesley from the board has failed, but there will be other opportunities -- and next time, the Players may be able to remove two birds with one stone. But for now, it’s the opposite side’s turn to make a move -- and thus, in the year 1794, Napoleon Bonaparte is placed under arrest when one of his political opponents, Saliceti, frames him for treason following the fall of Robespierre.

The Time Lords reluctantly provide the Doctor with a Time Ring and allow him to visit Europe during World War I to see for himself that his friends are safe. Sardon orders a technician to keep the Doctor under constant observation, but the technician soon grows bored and switches off, planning to check back in from time to time. Meanwhile, Sardon contacts a young and politically ambitious Time Lady, Serenadellatrovella, who is currently researching the life of a prominent Time Lord named Taskor who has suddenly vanished from public life. Serena attends a meeting with Sardon and his assistant, Luco, and although the CIA is never mentioned by name, Serena is under no illusions as to whom Sardon represents. Sardon explains that he needs someone to keep the Doctor under control, and that his backers will support Serena’s political career if she agrees to escort the Doctor on his mission. Serena accepts, but when Sardon shows her the Doctor, he finds that the Doctor is about to be executed by firing squad. Furious, Sardon has the Doctor yanked back to Gallifrey moments before the squad opens fire.

The Doctor reports that he encountered evidence of historical interference in Europe, and although Ragnar and Milvo refuse to listen to his wild stories, Sardon proves more interested. Luco has visited the 19th century undercover and has found evidence that unseen forces are tampering with the careers of both Wellington and Napoleon -- both for good and for ill, as if different factions are fighting for control of the two historical figures. The Doctor compares this to the incident he’s just witnessed, in which Count Ludwig Kroner and Countess Malika Treszka tried to alter history by changing the life of Winston Churchill; perhaps there’s some connection. He agrees to investigate, but is appalled when Sardon tells him that the Lady Serena will be accompanying him -- and that she’ll be piloting the Type 97 TARDIS that has been assigned to him. The Doctor has little choice but to agree to these terms, and Sardon orders him only to observe. Luco briefs the Doctor on the temporal locations of the interference traces, and the Doctor and Serena set course for 9 August 1794. Sardon is aware that the Doctor will ignore his orders, but since the Doctor is officially a renegade under sentence of death, Sardon can easily disavow all knowledge of his actions should he fail.

The Doctor’s new TARDIS takes the form of an ornamental fountain when it materialises at Fort Carre in Antibes, where a man named Citizen-Representative Latour has just arrived bearing orders for Napoleon’s immediate execution on multiple charges, including accepting bribes to sabotage the French military campaigns in Italy. The Governor has little choice but to obey, but before he can execute his prisoner, the Doctor and Serena arrive, posing as Citizen-Representative Henri Dupont and his aide, Marie Lebrun. The Doctor claims to have brought orders for Napoleon’s release, and he and Latour each accuse the other of being an impostor. Serena suggests that the Governor simply delay the execution until the truth is known, as it will be easier to execute Napoleon at a later date than it would be to restore him to life. When the Governor agrees, the furious Latour pulls out a pistol and tries to kill Napoleon himself, but he is himself shot by a new arrival -- the Countess whom the Doctor just encountered in 1915.

The Countess introduces herself as Madame Lefarge, a close personal friend of General Dumberbion, and presents the Governor with a letter proving beyond all doubt that the charges against Napoleon have been dropped. The Governor releases his prisoner with abject apologies, but the Doctor is still uncertain about the Countess’ motives; she seems to be interfering with history at whim, as if it’s all a game to her. The Countess privately warns the Doctor not to get in her way again; she and her colleague, Valmont, plan to ensure that Napoleon defeats England by sea and by land, and if the Doctor interferes, he will be killed. The Doctor and Serena leave the fort, pondering Serena’s warning, and see Valmont waiting for her in a carriage outside. The Countess joins Valmont and returns to the realm of the Players, where she is chastised harshly for killing Latour; however, she points out that Latour himself had chosen to intervene directly rather than act through agents, and that she was thus justified in taking direct action. She also claims that she’s allowed the Doctor to live because his presence makes the game more complicated and thus more interesting -- and an inside source has informed her that the Time Lords will take no action if the Doctor happens to be killed.

The Doctor has now worked out that the Countess is playing a game with human history. She had spoken of winning by sea and by land at a single stroke, and the Doctor realises that she intends to assassinate Wellington and Lord Nelson at the same time. The TARDIS data banks indicate that the two men met only once, at the Colonial Office on 12 September 1805, while waiting to see Lord Castlereagh, the Secretary of War. The Doctor and Serena visit the Colonial Office themselves, and catch sight of Valmont, disguised as a messenger, taking a package into the building. The Doctor pursues him while Serena distracts the guards; he is too late to prevent Valmont from handing the package to Wellington, but manages to convince Wellington that the package is a bomb. Wellington flings the bomb out of a window into a fountain, where it explodes harmlessly. Valmont vanishes into thin air before he can be questioned, and the Doctor, allowing Wellington to believe that he’s a British secret agent, advises him and Nelson to hush up the incident in order to avoid a public panic.

The Doctor and Serena return to the TARDIS, still with no idea what the Players’ ultimate goal is, if indeed they have one. The Doctor decides to see whether the Players are still interfering in Napoleon’s life; 1805 is a critical year, as Napoleon’s army is gathering at Boulogne, preparing to invade England once the British have been defeated at sea. Meanwhile, the Countess addresses her fellow Players, telling them that she has a plan for a Grand Design that will enable them to stage battles far greater than the small, petty games they’ve been playing with human history. Her fellow Players are intrigued, and agree to call a halt to the current game while the Countess and Valmont try to put the Grand Design into action.

The Doctor and Serena travel to Paris, rent a home on the Rue Chantereine, and establish themselves as rich and mysterious newcomers, hoping to attract the attention of high society and perhaps Napoleon himself. The Doctor learns from the TARDIS data banks that an attempt is due to be made on Napoleon’s life, and thus takes Serena to a café on the Rue Saint Honoré, where Napoleon’s carriage is due to pass by. A driver blocks the road with a wagon loaded with explosives, but the Doctor leaps into the driver’s seat and drives the carriage into a nearby fountain, where it explodes harmlessly. Napoleon recognises the Doctor and Serena from Fort Carre, and demands to know why he was subsequently unable to find out exactly who the Doctor is. The Doctor speaks vaguely and cryptically, and allows Napoleon to conclude that the Doctor is a member of the secret society known as the Illuminati who believes that Napoleon is a man of destiny. Impressed, Napoleon invites the Doctor and Serena to a reception at the Tuileries; his aide, Captain Hippolyte Charles, gets their address and arranges for the invitations to be delivered formally. The Doctor notes that they are followed home by Joseph Fouché, Napoleon’s spymaster, whose job is to ensure that they don’t pose a threat.

That night, the Doctor and Serena attend the reception along with other French aristocrats -- those who survived the Revolution, and those newly appointed by Napoleon. The Countess is also attending, as she has become one of Napoleon’s most trusted advisors; when she sees the Doctor, she warns him that the stakes of the game have increased, and repeats her warning that he will be killed if he stands in their way. Captain Charles then summons the Doctor to speak with Napoleon, and fetches the Emperor’s foreign minister, Talleyrand, to chaperone Serena until the Doctor returns. Talleyrand has a long history of switching sides whenever it’s convenient, but he tells Serena that he’s just doing what’s best for France -- and himself, of course. Talleyrand also tells Serena of the tempestuous relationship between Napoleon and Josephine; she once had an affair with Charles, but rather than punish Charles, Napoleon has kept him close at hand as a constant reminder to Josephine not to stray again. Talleyrand is approached by an American engineer named Fulton, but while he dismisses the man’s attempt to discuss his new invention, Serena notes that the Countess seems to have more of an interest in Fulton.

The Doctor speaks with Napoleon, claiming to be a scientist and traveller who has gained much knowledge on his travels, and vaguely hinting that Napoleon has a great destiny. He warns Napoleon not to trust the Countess, who will only serve him so long as their agendas remain the same. This jibes with Napoleon’s own feelings about her, and, trusting that the Doctor is on his side, Napoleon thus reveals that he has a plan to kill Lord Nelson before Villeneuve engages the British navy at Trafalgar. He offers to show the Doctor his secret weapon, but warns him not to leave Paris after he’s seen it. The Doctor returns to the reception, and is impressed despite himself to learn that Serena has spoken with Talleyrand for quite some time without giving away anything of her true identity or agenda. He is also interested to learn that Fulton is present, and he chats with the inventor, who is impressed by the Doctor’s technical savvy and offers to show him the secret weapon he is building for Napoleon -- a prototype submarine named the Nautilus.

The Countess is upset when she sees Fulton speaking with the Doctor, and contacts one of her associates to request that the Doctor be dealt with. As the reception draws to a close, the Doctor devours the tasty chicken pies on offer -- much to Serena’s displeasure, as the pies are stuffed with garlic. The Doctor and Serena then leave to find a carriage waiting for them outside -- but the driver is Valmont, who drives them out into the Gardens and tries to abandon them. The Doctor struggles with Valmont and manages to grab the whip out of his hands before he flees in the carriage. Moments later, the Doctor and Serena are attacked by a vampire, but the vampire recoils when it confronts the Doctor, repelled by the stench of garlic on his breath. The Doctor snaps Valmont’s whip in half and stakes the vampire through the heart, but is disturbed when the body then vanishes into thin air. The Doctor and Serena return on foot to the palace, where they claim that their driver tried to rob them, and Captain Charles arranges for a trusted driver to transport them back home.

The next morning, Fulton invites the Doctor and Serena to see the Nautilus, which is being stored in the stables behind the Tuileries. He admits to the Doctor that he doesn’t fully understand its propulsion system, which was designed by the Countess. The Countess then arrives and sends Fulton to an audience with Napoleon -- and privately confirms the Doctor’s suspicions that she intends to dispose of Fulton once his invention has served its purpose. The Countess tells the guards that the Doctor and Serena are British spies who must be held in the workshop until reinforcements arrive to arrest them, and moments later, a Raston Warrior Robot materialises in the stables. The Doctor and Serena try to flee, but the guards force them back inside -- and the Robot responds to the movement and attacks, killing both sentries. The sentries’ deaths attract attention, and soon the Robot is slaughtering its way through the ranks of French soldiers.

The Doctor grabs one of the Nautilus’ torpedoes, designed to work underwater, and shoots the Robot at close range with Serena’s help, blowing it to bits. The Countess returns, and is amazed to see the Doctor still alive -- but as the Robot begins to reassemble itself, she takes in the carnage and accepts that the Robot is too dangerous a weapon to use in this instance. She contacts her ally and has the Robot retrieved, and the Doctor watches with concern as the reassembled Robot vanishes into thin air. The Doctor informs Sergeant Lebrun that British spies tried to sabotage the Nautilus but blew themselves up with their own bomb, and Lebrun, unable to believe what he’s seen, decides to accept that version of events. As the Doctor and Serena depart, Fulton returns and informs the Countess that Napoleon wants to see the submersible in action by tomorrow, which will be impossible, as Fulton doesn’t understand how the Countess’ atomic drive works. In order to get the drive working on time, he suggests asking the Doctor for help.

The Doctor informs Serena that the vampire and the Raston Warrior Robot were transported from the Death Zone on Gallifrey via Timescoop, which must mean that someone in the CIA is working against them. He and Serena have warmed up considerably to each other since their first meeting, and Serena confesses that that CIA recruited her for this mission to keep an eye on the Doctor. They return to their home, but Valmont is waiting for them, and he holds Serena at gunpoint while the Countess orders the Doctor to accompany her to Boulogne and help to make the Nautilus seaworthy in time for its trial run. If he refuses, Serena will be killed. The Doctor has little choice but to go with the Countess, while Valmont holds Serena hostage, reminding her that he only needs the Doctor to think that she’s alive. As dawn breaks, however, Serena manages to distract the tired Valmont and escape into a nearby grandfather clock -- which is in fact their TARDIS.

According to Fulton, the Countess’ mysterious drive system is producing too much power and is thus mangling the gear assembly that’s supposed to run the ship’s propeller. The Doctor recognises the system as an omega drive and sets to work, with the Countess close by to remind him what will happen to Serena if he fails. The Doctor finishes his work just as Napoleon arrives, and the Countess, concerned that the Doctor may indeed have sabotaged the omega drive, orders him to accompany Fulton on the test run. Serena arrives too late to stop Fulton from launching, but while his submersible successfully dives underwater and destroys the test brig, it explodes on its way back to dock. Fortunately, the Doctor and Fulton survive, and the Doctor tows the shaken Fulton to land. Napoleon decides that the venture is too risky for him to waste any further effort on it, and the Doctor advises Fulton to abandon his submarine research and invest in steamboats instead.

Despite herself, the Countess is amused that the Doctor did indeed sabotage his work, risking his own and Serena’s lives to thwart her; however, she warns the Doctor that, while the Battle of Trafalgar will unfold as it did before, the game is not yet over. The Doctor and Serena conclude that the Countess must intend to assassinate Wellington before the Battle of Waterloo, but they have no further leads; thus, the Doctor decides to leap ahead to mid-July 1815, a month after the battle, to find out if and how the Countess changed history. The TARDIS materialises on a street in the middle of a victory parade, and the Doctor and Serena learn from a jubilant passer-by that Wellington died before he made it to the battlefield. However, Fouché’s spies are everywhere, and the citizens of Paris are too cowed to speak openly of the English duke’s mysterious death.

The Doctor explains to Serena that the French navy was defeated at Trafalgar, although Nelson died in the process. Napoleon turned his attention away from Britain and conquered Austria, Spain, and Germany; however, he then over-extended himself by sending his troops into Russia during the winter. Following this disastrous campaign, he was defeated and exiled to the island of Elba, but he escaped and was welcomed back to France as a hero. Wellington engaged Napoleon’s army in a number of battles, and the decisive victory took place near Waterloo. Napoleon was sent into permanent exile on the island of St Helena, where he died, possibly of arsenic poisoning. At least, that’s what should have happened -- but now history has taken a different course, and the Doctor and Serena must find out why.

To find out where things went wrong, they visit Minister Talleyrand, who is happy to see them once again. He agrees with the Doctor’s concerns that the Countess is exerting an unhealthy influence over Napoleon, urging him on to greater and greater conquests. Talleyrand also reveals that the Countess tried to enlist his help in a plan to assassinate Wellington before the Battle of Waterloo; however, while he’s wary of the Countess’ motives, he refuses to discuss her plan, since all has turned out well for France and the past cannot be changed. The Doctor offers to prove that neither of these things is true -- and then the Countess and Napoleon pass through and announce that they intend to attack Russia again, this time during the spring. The Countess does not openly challenge the Doctor and Serena, as she believes that she’s already won and that it’s too late for them to change things.

The appalled Talleyrand agrees to meet the Doctor and Serena at the Parc Montsouris at dusk so they can show him proof of what they say, but as they wait for him, they are arrested by police inspector Mercier, one of Fouché’s men, on charges of espionage. At the last moment, Talleyrand arrives, tears up the arrest warrant and sends Mercier and his men on their way. The Doctor and Serena then lead the amazed Talleyrand into the TARDIS and transport him fifty years into the future -- to find that Paris has become a devastated war-torn wasteland. According to a homeless old man on the street, a curfew is in force, and France has divided into individual city-states, all of which are at war with each other. When a patrol passes by, the homeless man turns in the three strangers, hoping vainly for a reward.

The Doctor, Serena and Talleyrand are taken for questioning by the soldiers’ Commandant, who turns out to be the Countess. Under her guidance, Napoleon conquered most of the known world, and when he succumbed to pneumonia, his empire collapsed into a loose collection of individual city-states. Each city-state is controlled by a different Player, and they have turned the world into a patchwork of miniature kingdoms, nothing more than a vast board on which to wage eternal war. The Doctor is appalled; at least the war games had an evil purpose, but this is just violence for its own sake. Talleyrand volunteers his services to the Countess, apparently accepting that the order of things has changed once again. The amused Countess offers a similar deal to the Doctor, and threatens to let her soldiers enjoy themselves with Serena if he refuses. She locks up the Doctor and Serena, giving them time to ponder her offer -- but once her guard is down, Talleyrand slips away, releases the Doctor and Serena, and takes them back to the TARDIS, where they return to 1815. Appalled by what he’s seen, Talleyrand tells the Doctor that, while trying to enlist his help in the assassination plot, the Countess spoke of the Duke dancing his last measure, and said that she who pays the piper calls the tune.

The Doctor and Serena travel back in time one month. Napoleon and his army are on the march, but before facing him, the Duke of Wellington is attending a ball in Brussels, hosted by the Duchess of Richmond. The Doctor and Serena gatecrash the ball, using a new CIA invention -- psychic paper, which causes the viewer to see whatever the holder wishes them to. The Doctor convinces Serena to introduce herself to Wellington; as he’d hoped, the Duke can’t resist the charms of a beautiful woman, and once Serena has his attention, the Doctor steps in. He reminds Wellington of their previous encounter and warns him that another assassination attempt is due; however, since he has no proof of his claims, Wellington dismisses his warning. Colonel Grant of the Intelligence division then arrives with grave news: Napoleon’s army has started marching earlier than expected, and Wellington will have to set off immediately and engage him in battle near Waterloo.

Before Wellington leaves, the Duchess of Richmond calls in the surprise entertainment, a full troop of Highland soldiers in full ceremonial dress who perform marches and military manoeuvres. The Doctor realises too late what the Countess meant by paying the piper, as Serena sees that one of the pipers is Valmont in disguise and throws herself in front of the Duke, taking a bullet through both her hearts -- a fatal injury so severe that it prevents her from regenerating. Valmont is overpowered and taken away, and the Doctor spots the Countess trying to slip away as well. He barely restrains himself from killing her on the spot, but as she is marched off, she asks the Doctor: what if it’s night after all? The Duchess promises to arrange Serena’s funeral, and Wellington, moved by her sacrifice, grants the Doctor permission to accompany him to Waterloo in case the danger is not yet over.

The next day, the Doctor observes the battle, and notes that Wellington and his allies are greatly outnumbered. When Wellington remarks that the outcome will depend on whether the Prussians or nightfall arrive first, the Doctor realises what the Countess meant -- and when Grant arrives to announce that the Countess and Valmont have escaped, the Doctor concludes that the Countess intends to deliver false orders to General Blücher, keeping him away from the field of battle. Since the French army is between the English and the Prussians, the Doctor decides to take the risky step of impersonating Napoleon, in the hope that most of the soldiers on the battlefield haven’t met Napoleon in person. Grant offers to disguise himself as a French lieutenant and escort the Doctor across enemy lines.

The Doctor and Grant successfully bluff their way through the French infantry and contact the Prussian reinforcements at Waivre. There, they convince Blücher that his orders have been forged, but as the Prussians prepare to set off, Valmont arrives at the head of a new wave of French troops. The Doctor rides out to meet them, once again posing as Napoleon; fortunately, this is General Didier’s first major command, and he is unfamiliar with the Emperor’s appearance. Valmont denounces the Doctor as an impostor, but Grant claims that this is an insult and challenges Valmont to a duel. Valmont, unused to direct combat, accidentally shoots off Grant’s hat, and, panic-stricken, vanishes into thin air when Grant takes aim at him. The Doctor informs the shocked Didier that his enemies are obviously using black magic against him, and the stunned Didier obeys the Doctor’s orders and returns to Waterloo instead of attacking the Prussians.

The Doctor and Grant return to Waterloo and report their victory to Wellington. When the Prussians arrive, the Countess realises that all is lost and abandons Napoleon to his fate. Napoleon sends in his fearless Imperial Guard, but they are cut down by British forces lying in ambush, and the remaining French troops are demoralised by the loss. The battle is over within hours, with history back on course, and the Doctor tells the grateful Wellington that England’s victory is reward enough for him. As he returns to the TARDIS, mourning Serena’s loss, the Countess stops by to congratulate him on a well-played game and reveals that the Games have been suspended indefinitely for fear of attracting unwanted attention. The Doctor insists that this was never a game to him -- in fact, the stress and trauma has caused his hair to go grey -- but the Countess departs, confident that they will play again in the future.

The Doctor pops ahead to 1816 to ensure that history is back on track, and in the process, he wins some money in a faro game and invests it in a bank owned by one of the Prince Regent’s friends. He then returns to Gallifrey to report success to Sardon and Luco, and reveals that someone used a Timescoop to send a vampire and Raston Warrior Robot to Earth in order to kill him. And Luco had already visited the Napoleonic era once before to investigate the interference. Luco scoffs, but inadvertently gives away the fact that he knows what the Timescoop is; presumably, he made contact with the Countess on his earlier visit, and allied himself with her in order to discredit Sardon and move into his position once this mission failed. Sardon has the protesting Luco taken away for interrogation by mind probe.