Final Sacrifice ( comic story ) Final Sacrifice was the concluding story of the arc begun in " Doctor Who " ( 2009 ) # 1 . It was the last story of that publication and ended the Tenth Doctor ' s continuous run in IDW Publishing ' s comics . It also wrote out the IDW - only companion s , Matthew Finnegan and Emily Winter , and served as a semi - sequel to an early one - shot story , " The Time Machination " . Publisher ' s summary . Part one . On a war - ravaged alien world , the Doctor and Emily fight to save Matthew from the Advocate , while avoiding a planetwide civil war and a space - and - time misplaced Edwardian Torchwood , still hunting the Doctor since The Time Machination ! Everything leads to this point — but who will die ? Part two . Long live the Queen ! As the war between the Soul Free and the Terror builds , the Doctor discovers who ' s really pulling the strings behind the scenes ! And as " Mr Finch " faces off against Emily , Alexander Hugh and the Edwardian Torchwood agents choose their own sides in the coming war . . . Part three . War ! What is it good for ? ! The Doctor discovers the truth about Kol ' Ne Wah and finds Matthew , while Emily and Hugh try to stop the world from rebooting ! But what is the Advocate ' s terrible plan - and why are the fifth - dimensional Tef ' Aree involved ? Part four . Tragic loss . . . Final issue ! Final appearance of the Tenth Doctor ! Sad farewells . A song ends . People die . What , you thought we ' d end on a high note ? It ' s called " Final Sacrifice " , guys ! Multiple Eagle Award - nominated writer Tony Lee and Matthew Dow Smith close the book on the tenth Doctor . . . Plot . Oxford University , 1906 , and Robert Lewis and his colleague Eliza Cooper of Torchwood visit Professor Alexander Hugh and his assistant Annabella Primavera to take part in a demonstration of a time machine built from cannibalised alien technology . However , their first trip takes them to a war - torn alien world , and straight to the Doctor and Emily . Their arrival attracts attention and soon the whole group is arrested by the Soul Free . They are observed by the Advocate who has completely brainwashed Matthew against the Time Lord . The planet has been fought over for thousands of years by the Soul Free and the Terror Farmers , who both claim it as their home . The proof lies in a sealed temple called Kol ' Ne Wah . The Soul Free are led by Finch , now calling himself Lau ' Tan , who claims he now opposes the Advocate , and who explains that the device that the Advocate took from the TARDIS was created by the Tef ' Aree . Just then they are attacked by the Terror Farmers , Annabella killed , despite the Doctor ' s insistence that she was supposed to live , and Lau ' Tan wounded . However , he is fit enough to disguise himself as the Doctor and turn himself in with the now captured Emily . As Matthew begins to realise the true nature of the Advocate , she commands Emily and Lau ' Tan to fight to the death . Emily and Lau ' Tan attempt escape but are overpowered and thrown in cells . The Doctor , meanwhile , leads his group to the Temple of Kol ' Ne Wah . While Matthew realises he ' s been duped and enlists Lau ' Tan ' s help in putting things to rights , Emily receives a visit from the Tef ' Aree who tell her that she must stop the Advocate ' s device which " reboots " planets , but in order for the device to be stopped it must first be started . Matthew rescues her , but it soon transpires that this is Lau ' Tan in disguise , sent by Matthew to get Emily to safety and give her Turlough ' s faked diary while he spies on the Advocate . At the temple , the Doctor ' s party enters and quickly see that it is in fact a spaceship . The Time Lord is intrigued by the mix of technology and takes a harddrive from the ship . However , as they leave , they are ambushed by the Terror Farmers . While Robert Lewis is enlisted into the service of the Advocate , the Doctor and Professor Hugh make the safety of the TARDIS and listen to a heavily degraded message on the harddrive from Earth Colony One , a lost and misplaced expedition , who made contact with the Tef ' Aree and were given a terraforming device with which they hoped to make the colony self - sufficient . But the Doctor realises that the Terror Farmers ( Terra Firma ) will defeat the Soul Free ( Sol Three ) and become the Terranites . The Doctor realises that the Advocate plans to use Matthew ' s un - irradiated human DNA to reactivate the terraforming device which will wipe out the whole planet even as they head into war . In his cell , Matthew receives a visit from the Tef ' Aree and suddenly understands everything : his and Emily ' s sacrifice will save the planet . He and the Advocate teleport up to the orbiting terraforming device and the Doctor follows in the TARDIS , but not before he has put Professor Hugh down in the middle of the fighting to urge the two sides to get to safety aboard the colony ship . However , Lewis won ' t listen . As the Advocate tries to get Matthew to activate the terraforming device , he finally reveals his true allegiance . She shoots him and uses his palm to activate the device . Squabbling on the ground between the Terror Farmers and the Soul Free is brought to an instant end as the device begins to erase anything that wasn ' t on the planet a few thousand years before . They all run for the temple . The Doctor confronts the Advocate , but she reveals that she has rigged the terraforming device such that only Matthew can switch if off , and if he does it will kill him . Robert Lewis destroys the colony ship ' s force field which protected it from the terraforming device then makes to shoot Eliza who sided against him with the Doctor . Emily jumps in the way and falls to the ground . Now the Advocate wants to know if the Doctor is prepared to sacrifice his other friend or the entire planet below . Emily recovers , saved from the blast by Turlough ' s diary while Robert Lewis is destroyed by the terraforming beam . The force field around the colony ship cannot be repaired , but Lau ' Tan realises it can be replaced . He transforms himself to replace the damaged component and restart the shields while Emily gets everyone safely inside . Matthew distracts the Doctor , grabs the Advocate and slams his hand onto the terraforming controls . He and the Advocate die instantly , but the device is deactivated . The Doctor takes Matthew ' s body to the surface of the planet where a Tef ' Aree appears and tells him and Emily that it was once Matthew , transformed through sacrifice and the merging of energy with the Advocate into a fifth - dimensional being . He gave the Earth colonists the technology and created the Advocate so that his human self could one day be empowered and become the Tef ' Aree . The Doctor is appalled by the level of manipulation , but the Tef ' Aree is unmoved and vanishes . Eliza elects to remain on the planet and help to rebuild it . The Doctor takes Professor Hugh and Emily back to Oxford , 1906 , in the TARDIS . Here he explains that Annabella Primavera , like Emily , was a fixed point in time and space , but while Emily was supposed to have died , Annabella was supposed to have lived . Emily must now take her place to mend the web of time . It was Annabella who discovered Archie Maplin and eventually set up United Actors in Hollywood . The Doctor heads off for an adventure on Mars . . .