History of the Doctor Who Universe
The Talons of Weng Chiang (exposition from the original series episode)
The Year 5000
Another Ice Age affects Earth at this time, and the world is organized into a number of "Alliances." In this era, the Icelandic Alliance and the PacBloc are at war. The Icelandic Alliance is a peaceful 51st Century power, but falls when its Commissioner is assassinated by Magnus Greel's Peking Homunculus. The Peking Homunculus is an artificial being with the brain of a pig intended as a child's companion - it goes rogue and assassinates the Icelandic Alliance's commissioner, almost causing World War VI. The Supreme Alliance comes into power, with a man named Magnus Greel as its Minister of Justice. He is responsible for the deaths of 100,000 enemies of the state, earning him the epithet "The Butcher of Brisbane".
The Supreme Alliance commits a number of war crimes and is brought down by the Filipino Army at the Battle of Reykjavik, at which the Doctor is present. Greel, who has been experimenting with time travel, flees to 19th century China by means of a time cabinet which utilises zygma beam technology, taking The Peking Homunculus with him.
Emotional Chemistry (BBC books - excerpted from the Doctor Who Reference Guide)
Lord General Razum Kinzhal is preparing to set in motion the closing stages of the world war. More than the enemy, his fellow generals of the Icelandic Alliance fear what such a man might do in peacetime. The brilliant strategist Razum Kinzhal has devised a complex plan to rout the PacBloc forces and destroy their leader, the evil Karsen Mogushestvo. The plan appears to go fatally wrong when Kinzhal and his young adjutant, Angel Malenkaya, are captured while scouting out Mogushestvo’s defences at Omsk -- but when Mogushestvo tries to “interrogate” Kinzhal by cutting into his brain with a neural scalpel, he triggers a hidden neural trap which stuns every living being in the vicinity except Kinzhal. Kinzhal and Angel flee from Omsk in a stolen Stepperider, but run over a field of heat-sensitive mines and must fire their plasma cannon to distract the mines by creating a new heat source. Mogushestvo detects the heat flare and, aching from his humiliation, sends his robot air force out to destroy Kinzhal; however, Kinzhal and Angel abandon the Stepperider at the last moment and watch from a safe distance as Mogushestvo’s air force is destroyed in turn by the Icelandic Alliance’s own robot drone planes. Once again, Kinzhal has demonstrated his tactical genius by scouting out Mogushestvo’s defences and destroying his entire air force in one move. Only chance does not factor into his calculations, but he claims that Angel acts as his good luck charm. While she doesn’t understand everything Kinzhal is telling her, Angel is nevertheless deeply in love with him...
...Aphrodite then must explain her nature to the Doctor, who is shaken to learn that Dusha and Kinzhal are two halves of the same being -- a Magellan, a creature like a sentient star. Aphrodite’s parents broke a serious taboo by giving birth to a child, and Aphrodite claims that the Doctor defended them at their trial; however, he has no memory of doing this, and realises that it happened either in his forgotten past or in his future. In any case, they were punished by being exiled to two separate time zones. Kinzhal is the intellectual side of the Magellan, and Dusha the emotional. The horrified Doctor realises that if Kinzhal and Dusha are put in mental contact as planned, their reunion will restore them to their original state -- and the Earth of the 51st century will be consumed in flame as the reunited Magellan absorbs the planet’s mass and energy to recreate its original form...
...The Doctor, realising that Kinzhal will continue his war in the 51st century unless he is reunited with Dusha, decides to continue with the original plan while he tries to think of an alternative...
...In the 51st century, Wargaard’s forces move in on Omsk, leaving Sverdlovsk undefended -- or so it seems. Though there’s no sign of Kinzhal’s forces, Mogushestvo sends his own army in to destroy Sverdlovsk, confident that they will be finished their work before Kinzhal can show his hand. But Kinzhal has buried tanks beneath the snow at Sverdlovsk’s intersections so they show no heat signatures until their modified engines fire, venting exhaust blasts of plasma fire hotter than the sun at the invaders. In Omsk, Mogushestvo watches in shock as his forces in Sverdlovsk are eliminated -- and Kinzhal’s forces then make their move on Omsk. The tanks were shut down and dragged across country by cloaked horses, and the movement thus did not register on Omsk’s heat-sensitive scanners until the tanks were practically within the city already. Omsk is overrun, and the defeated Mogushestvo vows to go down fighting. Meanwhile, de Schalles slips away from the front lines at Sverdlovsk and heads for Tobol’sk, aware that Kinzhal’s plan is succeeding -- which is why it’s so important that he be killed.
As Kinzhal, Wargaard and Wargaard’s aide observe the progress of the battle, Fitz and Aphrodite arrive at Tobol’sk, bearing the locket which will link Kinzhal to Dusha. The Doctor arrives and offers Kinzhal an alternative to the destruction of Earth. Due to the war, Earth currently has no space programme, but the Doctor can use the TARDIS to move Kinzhal through space but not time to an uninhabited planet which can serve as fuel for the Magellan’s reunion. However, Kinzhal considers even space travel in a time machine as being too risky, and since zygma energy is at its most elastic through the dimensions of Time, there is a good chance that the power of the Misl Vremnya will not reach to another planet. He thus rejects the Doctor’s plan, leaving no alternatives but the destruction of the world either by the reunion of the Magellan or by Kinzhal’s waging eternal war on its surface.
Angel arrives to report victory to Kinzhal, and overhears the conversation between him and the Doctor. At the same time, de Schalles and his followers burst into the war room to assassinate Kinzhal. Wargaard’s aide shouts out a warning, Angel takes a bullet while shielding Kinzhal from attack, and Aphrodite, responding to the emotions around her, attacks de Schalles and snaps his neck. Realising that she is dying, Angel offers to take Dusha’s spirit into her own body, knowing that Dusha will be able to heal the injuries; Angel will die, but her body will live on as a host for Kinzhal’s lover. Taken aback by this demonstration of selfless love, Kinzhal accepts this as a suitable alternative.
He thus promises to spare the Earth, and offers to use the transit belts to establish an army of Time Agents (just as Magnus Greel predicted) who will police and protect the past.
He goes to war when he was just a boy (presumably one of the ones above - meaning he was probably born in the end of the 50th century, although Torchwood, "Kiss Kiss Bang Bang" makes a reference to Jack living in the year 5094 and the events of "Emotional Chemistry" could take place later during the 51rst century) and was with his best friend when they got caught crossing the border over enemy lines and they tortured his friend rather than him because his friend was weaker. They made Jack watch him die, and then they let him go. When Jack is asked which enemy he’s referring to, he says they’re the worst possible creatures you can imagine. Jack admits that he persuaded his friend to join up because he thought it would be an adventure. (Torchwood, "Capatain Jack Harkness")
Jack was the first to join the Time Agency from his home in the Boeshane Peninsula which prompted his nickname at the academy: The Face of Boe (Doctor Who, "Last of the Timelords")
Jack is aware of the 51st-century weapons factories of Villengard, and is surprised to learn that the Doctor is responsible for blowing up the weapons factories; now they’ve been replaced with banana groves. (Doctor Who, "The Doctor Dances")
He is aware of the Dalek fleet disappearing to fight the Time War. (Doctor Who, "The Parting of the Ways")
The Time Agency took two years of Jack’s memories away from him while he was still an Agent himself, and he has no idea what he did in that missing time. He becomes a con-man to try and gain the resources to recover his lost memories. (Doctor Who, "The Doctor Dances")
Jack apparently initially has a partner during his con-man days - another rogue Time Agent known as Captain John Hart. Much more amoral than Jack, the two spend 5 years together in a time-loop stretching across two weeks. (Does this mean they experienced the time-loop 130 times?) (Torchwood, "Kiss Kiss Bang Bang")
Jack obtains a Chula ship and the last Chula War Ambulance, and "parks" the ambulance in 1941 during the London blitz. (Doctor Who, "The Doctor Dances")
Jack Harkness is not really his name, he simply adopts it, although he didn’t realise how ’hot’ the original was. He only chooses the Captain’s name because it is convenient - which means the real Captain is going to die in battle. (Torchwood, "Captain Jack Harkness")
After traveling with the Doctor, Jack is killed and resurrected on the Game Station in the year 200,100. (Doctor Who, "The Parting of the Ways")
Jack explains that after the events on the Game Station the last time he met the Doctor, he used his now broken Time Vortex Manipulator to return to Earth in 1869, living through the 20th Century until he found a version of the Doctor he could happily coincide with. (Doctor Who, "Utopia")
The above means that there were at least 3 versions of Jack in 1941 at the same time as of the events in "Captain Jack Harkness" The Time Agency seems to have better technology than the failed zygma energy experiment, but Jack seems to end up at around the same time that Greel did when he escaped to the past.
Jack apparently either continued his con-man routine to survive at least into the first World War, or was involved in that war during his initial con-man days before meeting the Doctor. (Torchwood "Small Worlds") In any case, he survived through the twentieth century and could have kept tabs on the Torchwood project from it's inception by Queen Victoria. He says that he "kept an eye on Rose" during that time and eventually, somehow, does indeed become the head of Torchwood 3.
The Time Agency eventually gets shut down, and Jack Harkness and Jack Hart are only 2 of 7 Agents left. (Torchwood, "Kiss Kiss Bang Bang")
The Invisible Enemy (original series episode - synopsis from Wikipedia)
While the Earth is having it's problems, mankind has been colonizing space at a fantastic rate. Some human space travelers are cruising near the outer planets of the solar system with their ship on autopilot. The ship's computer, and soon the human crew, is possessed by a strange virus. Reaching their destination, Titan Base, they proceed to take over the base as a breeding ground. The station manager, Lowe is able to send out a distress call.
The TARDIS is traveling through the same region, and is infected by the virus. The infection passes to the Doctor, but he is unaffected for the moment. He and Leela hear the distress call and go to investigate. While there, the Doctor is overcome by repeated infections and is chosen, due to his incredible powers as a Time Lord, to be the host of the Nucleus of the Swarm. Leela is unable to be infected.
The Nucleus declares her a reject and orders that she be killed. The Doctor manages to break free of his infection and tells Leela how to get the TARDIS to the nearest medical center. Accompanying them is Lowe, who has been infected, although the Doctor and Leela don't know this.
At the medical station, the Doctor's doctor, Professor Marius, introduces the group to K-9, a robotic dog he made to replace the real dog he had to leave on Earth. Professor Marius is baffled as to how to treat the Doctor's strange infection. Meanwhile, Lowe has been infecting the staff of the hospital.
Leela and the Doctor decide on a last-ditch strategy. They create clones of themselves, which can only survive for ten minutes due to problems with the technique. The clones will then be shrunk and inserted into the Doctor. There they will destroy the Nucleus and escape through the tear duct. In the meantime, Leela and K-9 fight off the infected staff of the hospital.
After a hazardous voyage through his mind, the Doctor's clone and Leela's clone are separated, and the Doctor's clone reaches the Nucleus. He has no weapons with which to destroy it, and it learns the intended escape route of the Doctor's clone, since the Doctor thought of it. Prof. Marius faithfully retrieves something from the tear duct and expands it to human size. It turns out to be the Nucleus. The Doctor is cured of his infection.
The Nucleus and the infected staff leave for Titan Base so the Nucleus can spawn. The Doctor realizes he is cured since Leela's clone introduced into his blood stream her immunity factor. He replicates it and gives it to Prof. Marius. The Doctor and Leela and K-9 proceed to Titan Base in the TARDIS.
They just barely manage to fight off the infected humans, but are again without sufficient weaponry to destroy the Nucleus, or its many children which are about to hatch as "macro-sized" beings, like the newly macro-sized Nucleus. The Doctor manages to jam the door they are behind and rigs a gun to fire into a cloud of Oxygen gas he is releasing and escapes. As intended, when the Swarm finally forces open the door, the blaster fires, igniting the Oxygen in Titan's methane atmosphere and destroying the Swarm and the base.
When they return to the hospital, they thank Prof. Marius for the use of K-9, who has ably assisted them. Prof. Marius makes a surprising offer. He must soon return to Earth, and weight restrictions now prevent him from taking K-9 back. He offers him to the Doctor, with some sadness, but knowing K-9 will have a good home. The Doctor and Leela gratefully accept, and K-9 himself is eager to learn more about the TARDIS.
Prof. Marius, with teary eyes, watches the TARDIS disappear, commenting, "I only hope he's TARDIS-trained."
The Keep (Comic Strip from the Doctor Who Magazine Issue # 248-249 - from the Doctor Who Reference Guide)
An SOS summons the Doctor and Izzy to 51st-century Earth, which has been abandoned by the rich and powerful as the sun goes nova. Those left behind have fractured into millions of nation-states, warring through the ether in battles conducted via transmat. Only one place on Earth is safe from the wars -- the transmat-shielded Keep, the source of the SOS. Inside, the Doctor and Izzy find a prototype plasma sun called the Cauldron, created by the scientist Crivello. Crivello’s robot servant Marquez unexpectedly throws the Doctor into the Cauldron, but the Doctor emerges unscathed, having made a psychic link with the living sun.
The Idea of the Magellan and the living sun from this story seem to tie in with the 10th Doctor television episode "42", which also featured a sentient star. The Earth being abandoned during the 51rst century would seem to tie in with the solar flares that caused the Ark to be sent in it's orbit of the solar system as told in the 4rth Doctor television episode "The Ark in Space" .