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this is a recap of most of the series 3 finale without any real focus on the invasion and its aftermath. Seriously, why is there so much detail about the Master killing Chantho?
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The Toclafane invasion would have occurred in the early 21st century on Earth, but due to the actions of the Tenth Doctor, Martha Jones and Jack Harkness, the invasion never took place (see The Year That Never Was).
Origins
The origins of the Toclafane Invasion lay in the Tenth Doctor and Martha Jones refuelling the Tardis with energy from the Cardiff rift. Jack Harkness spotted the TARDIS and jumped on it, sending it to the year 100,000,000,000,000. There, the last humans were preparing to board a ship that would take them to Utopia. Martha, the Doctor and Jack went to the base where the ship was being built where they met Yana and Chantho.
The last humans boarded the ship but the rocket needed to lift off. Jack went into a room and lifted canisters that helped let the ship go into space. Martha was talking to Yana and Chantho about the Doctor. While they were listening to Jack and the Doctor, Yana started to hear drumming.
Yana opened a watch that was actually a Chameleon Arch. He discovered that he was the Master. Yana killed Chantho and stole the TARDIS. The Doctor reached the room and locked it to the last place where the TARDIS went: Cardiff 2007. (TV: Utopia / The Sound of Drums)
The Election
The Saxon Master on the day the trio arrived was elected Prime Minister of the United Kingdom under the name of Harold Saxon. He had married and run for Prime Minister since the downfall of Harriet Jones. Martha contacted her family to make sure they were safe. Martha's parents were being watched by an agent hired by "Saxon" called Miss Dexter.
The Doctor, Martha and Jack later found a way onto the Valiant and found out that at 8.02am the Toclafane were going to invade. They witnessed President Winters get killed by a Toclafane and the Doctor get hit by the Master's laser screwdriver. The Doctor aged 900 years in human form. Jack was killed repeatedly by the Master.
Martha then teleported to Earth using Jack's vortex manipulator and witnessed millions of Toclafane wreak havoc. (TV: The Sound of Drums)
The Year That Never Was
Martha Jones spent the year in between May 2008 and May 2009 travelling the world. Alien races and invaders did not go to the planet because the human slaves were building missiles that would destroy them. On board the Valiant, Francine, Tish, and Clive Jones were slaves of the Master. Jack Harkness was chained up in the engine room, and the Doctor remained on the ship living inside a tent and was forced to watch whatever the Master did.
Martha met with Tom Milligan, a doctor who was seeking to repel the Toclafane. They travelled to Professor Allison Docerty's lab and took a Toclafane hostage in order to discover the species' true identity. Upon capturing a Toclafane and opening up its armoured shell, they discovered that the Toclafane were the humans from the year 100,000,000,000,000 and the Toclafane that Martha captured had the memories of Creet, a young boy from planet Malcassairo whom Martha had met and liked. The Toclafane said that the legends had lied to them; that there were no diamond-skies in Utopia, only "darkness, the never-ending darkness" and then out of despair the humans regressed into sadistic, but child-like, states and integrated themselves into armoured shells, becoming the Toclafane. They travelled with the Master to a void between dimensions, where they ultimately invaded Earth in 2008. When Tom Milligan asked why the Toclafane were slaughtering humanity, as humans and Toclafane were one and the same, the Toclafane sniggered and said, "Cos it's fun." Tom, horrified, shot the Toclafane.
The next morning, the Master planned to launch the entire Toclafane fleet towards the Universe itself, as he had plans to rule the entire universe and create a new Empire. Martha travelled to London to stop him, but she was caught by the Master, who had been aware of her presence. Thus she was taken to the Valiant once again and made to watch as the Master prepared to commence his war. He revelled in his apparent victory, until Martha revealed her plan that when humanity thought the word "Doctor", the power would make the Doctor whole again. This occurred and Jack led the guards to the TARDIS just as the Toclafane were about to leave Earth to invade the cosmos. Jack Harkness destroyed the Toclafane guarding the TARDIS and destroyed the paradox machine successfully. The Toclafane vanished from the skies of Earth and were teleported back to Utopia and thus they never invaded. (TV: Last of the Time Lords)