Dr Who Episode 162 "The End of the World" - Earth, 5 billion years into future.
Earth destroyed by supernova. Saves trapped dignitaries from bad case of sunburn including an alien calling himself "The Face of Boe". First mention of "Bad Wolf" the mysterious happening tracking the Doctor through time and space. No one notices.
Dr Who Episode 163 "The Quiet Undead" - Earth, Cardiff, 1869
The Spacial Rift in Cardiff forced open by an Alien Species called the Gelth. Rift closed by servant girl Gwyneth who dies in the process. She is a direct predecessor of Gwen Cooper of Torchwood 3. Next mention of "Bad Wolf". No one notices again.
Dr Who Episode 164 "Aliens of London", "World War Three" - Earth, London, 2005
Slitheen invade London. Doctor interacts with Toshiko Sato who is later recruited to Torchwood 3 and Harriet Jones a low level backbench MP. "Bad Wolf" mentioned again. Still no one notices.
Dr Who Episode 168 The Empty Child", "The Doctor Dances" - Earth, London, 1941
Doctor interacts with Capt Jack, a time agent so desperate to retrieve 2 years of memories stolen from him, he almost exterminates the human race. Redeems himself by sacrificing his time ship to stop a German World War 2 bomb labelled "Bad Wolf", (No one notices again), from making the situation worse. Joins Doctor and Rose in Tardis.
Dr Who Episode 168 Boom Town - Earth, Cardiff, 2005
Doctor, Capt Jack and Rose Arrive The Rift to refuel The Tardis. The landing zone will eventually become the front entrance to Torchwood 3. Discover a surviving Slitheen is planning on Building a Nuclear Power Station called "Blaidd Drwg" which is Welsh for "Bad Wolf". Finally the Doctor takes notice but says it is all a coincidence. Tries to stop the plot but causes the Rift to open. Manages to close it but it is now unstable.
Dr Who Episode 170 "Bad Wolf", "The Parting of the Ways" - Orbit of Earth Millions years in the Future
Finally "Bad Wolf" is revealed. "The Daleks" are back. After exterminating everyone including Capt Jack, they turn to exterminate the Doctor but, Rose saves the day by channelling the temporal power of the Tardis. Out of control she brings Capt Jack back to live. To save Rose's Life The Doctor absorbs the energy and is forced to re-generate. The new Doctor leaves Capt Jack behind.
Not Directly in Cannon, but mention in later episodes
Capt Jack uses a portable Temporal Transporter to go back to Cardiff and The Rift where he knows the Doctor will eventually arrive to refuel the Tardis. A miscalculation sends him to the 1800's with a broken Temporal Transporter. As he waits for the Doctor, discovers he cannot die.
Dr Who Episode 171 "The Christmas Invasion" - Earth, London 2006
Doctor arrives very ill due to a bad regeneration. Harriet Jones is Prime
minister, Earth invaded, Doctor does battle but his hand is cut off in the process. Fortunately he still has enough energy to grow a new one. The amputated hand mysteriously disappears. Harriet Jones orders Torchwood to destroy the space ship. The Doctor being angry brings down Harriet's Government using 6 words "Don't you think she looks tired?"
Dr Who Episode 172 "New Earth" - New Earth, 5 billion years into future
Bumps into "Face Of Boe" who tells him he has a message for the Doctor. He teleports away without delivering message.
Dr Who Episode 173 Tooth and Claw - Earth, Scotland, 1879
Saves Queen Victoria from an Extra Terrestial Werewolf. In gratitude, she bans the Doctor and Rose from the British Empire and establishes Torchwood (anagram of Doctor Who) with two mandates. Defend the British Empire from Extra Terrestial Enemies (which includes The Doctor) and "Anything Alien Belongs To Us"
He bumps into Torchwood in different guises until...
Dr Who Episode 181 "Army of Ghosts", "Doomsday" Earth, London 2006
Torchwood 1, located in Docklands, London, opens a dimensional rift allowing first the Cybermen and then the Daleks to invade Earth. The two alien species unable to form an alliance, battle amongst themselves destroying Torchwood 1 in the process. Out of about 2000 personel only 93 survive. It becomes known as the "Battle of Canary Wharf". Amongst the survivors are Ianto Jones who secretly smuggles out his girlfriend Lisa a partially converted Cyberwoman. Rose takes a one way trip to a parallel Earth. where she says her last goodbyes in the parallel Country of Norway in a place called Darlig Ulv Stranden which is Norwegian for "Bad Wolf - Bay"
The Doctor is now alone.
Not Directly in Cannon, but mention in later episodes
Capt Jack rebuilds Torchwood in the Doctor's Honour. Torchwood 3 is sited of Cardiff Rift. Primary mission is to protect the Rift which has become very unstable and hopefully finding "The right Doctor" to try and cure his immortality. Using the Doctor's amputed hand recovered from Torchwood 1, he rigs it to detect the Doctor's presence near the Rift. Recruits Ianto Jones, Gwen Cooper,Dr. Owen Harper and Toshiko Sato.
Dr Who Episode 185 "Gridlock" New Earth, 5 billion years into future.
The Doctor and his New Assistant Martha Jones, whose cousin, Adeola Oshodi, who worked for Torchwood 1, was one of the first victims in the "Battle of Canary Wharf", Saves the population of New Earth from Destruction with the help of "The Face of Boe". Boe delivers his last message before his death. "You Are Not Alone".
Torchwood Episode - "End of Days" Earth, Cardiff, 2006
After the events involving Abbadon, Jack notices the servered hand glowing.
Dr Who Episode 185 "Utopia", "The Sound of Drums", "Last of the Time Lords" - End of the universe, A couple of thousand years before Our Universe Ends, Earth 2006
The Doctor lands on the Rift for refueling and sees a very angry Capt Jack running towards the Tardis carrying a severed hand. The doctor aborts refuelling and takes off but Capt Jack grabs the outside of the Tardis forcing the Tardis to travel to the end of the Universe. The three travellers help out a person called the Professor. He turns out to be "The Master" last seen in the American TV movie. "The Face of Boes" message was correct.
Unfortunately the Time War with the Daleks and his enforced exile has made him a) very angry and b) totally insane. He steals the Tardis but not before the Doctor has locked the co-ordinates so that the Tardis can only return to its last location plus or minus 18 months. The Master is also forced to regernerate.
Repairing Capt Jack's portable Temporal Transporter they return to Earth 2006 to find that due to the fall of Harriet Jones' government a new government has been formed by Mr Harold Saxon an alias for "The Master". He neutralises Torchwood by ordering them on a wild goose chase in the Hymalayas, Exterminates the entire cabinet, enslaves the planet and keeps The Doctor and Capt Jack as his playthings. Only Martha Jones escapes and on her own she carries out the Doctor's plan and eventually the Master is defeated and killed. Or is he...?
Capt Jack hops a lift back to Cardiff with the Doctor. The Doctor tells him he cannot reverse the immortality effect. Jack tells the Doctor what he is really afraid of is growing old and losing his good looks. On his homeworld he was so hansome he was known as The Face of Boe. The Doctor says he will be known by that name again and bids goodbye. Martha Jones decides not to stay with the Doctor as it is way too dangerous.
Once again he is alone.
Future Episodes of Dr Who and Torchwood
Capt Jack recruits Martha Jones to join Torchwood.
Capt Jack and Martha rejoin the Tardis for another adventure with the Doctor.