Cold Blood ( TV story ) Cold Blood was the ninth episode of the fifth series of BBC Wales " Doctor Who " . It was written by Chris Chibnall and was the second part of a two - part story that featured the return of the Silurian s and the death of recurring companion Rory Williams , which soon escalated further to total erasure from existence after a crack consumed his body . Thus only the Doctor remembers him . Once more , the Doctor is seen trying to bring about a peaceful solution to a conflict between Silurians and human s . In this case , a rogue Silurian is responsible for the breakdown of trust , as is just one human . It ' s worth noting that unlike the previous branches of the Silurians , which had a more peaceful nature , Alaya and Restac are shown to be racist and genocidal . Unlike the previous branches of the Silurian species , which never survived their initial encounters with the Doctor , this one found in Cwmtaff survives for another chance at cohabitation with humanity in the future . Neve McIntosh , who plays Alaya and Restac , would later return to the show the following year in " A Good Man Goes to War " , playing another Silurian named Madame Vastra . However , unlike the characters in this story , Vastra would serve as one of the Doctor ' s recurring allies , primarily the Victorian Era Synopsis . Once more the Eleventh Doctor meets members of the Silurian race . However , this time , can he prevent them from being destroyed by human ity out of an act of self - presevation , or can he broker peace between them and bring about a better future for both races of planet Earth ? In the meantime , there are other questions that are left unanswered : Can Ambrose be trusted to keep Alaya alive ? What is happening to Tony Mack ' s wound ? Are the Silurians responsible for the empty graves ? And what awaits Mo and Amy when a Silurian doctor is eager to see what makes them tick ? Plot . A view of the Earth is shown from space as the sun rises from behind it , illuminating the features of the planet . A Silurian narrates that his people are now awakening in 3020 , and that he remembers the day 1000 years ago when he met the Doctor and the loses that the Time Lord suffered because of failed attempt to negotiate peace . Back to the present day in 2020 The Doctor and Nasreen enter the Silurian city , which is quite elaborate and grand . A curious Nasreen wonders how any of the vegetation and the city itself could be there , being so far beneath the Earth . The Doctor explains that the city and the vegetation are fueled by thermal energy and most of the Silurians are hibernating in suspended animation . To get back who was taken ( Mo , Amy and Elliot ) , they need to find the Silurians that were awakened by the threat the drill posed to the city . Nasreen wonders if waltzing straight into the city is a good idea as the Doctor assures her that the " front door approach " is always the best idea . An alarm goes off , announcing hostile life forms entering the city . Shocked at being called hostile , the Doctor admits that the " front door approach " may not have been the best idea . They turn to leave , but Silurian soldiers arrive and hold them at gunpoint . The Doctor tells them they are not hostile , but the Silurians knock them out with gas . Amy and Mo are strapped to surgical operating tables in a Silurian surgery . The Silurian surgeon , Malohkeh , is getting ready to dissect Amy . He removes his mask and tightens Amy ' s straps . Malohkeh notes that Amy is reacting differently to the cold than Mo ; Amy yells she was dress for Rio . He then takes the scalpel and begins to put it in Amy ' s chest , but is called away to examine the Doctor and Nasreen . Amy , who has sneaked the remote controlling the surgical tables from the surgeon , releases Mo and herself and they escape into the city . While searching for a means of returning to the surface , they find Elliot , trapped in suspended animation , but alive . The Doctor and Nasreen are strapped to tables in a separate laboratory and forcibly scanned ; while Nasreen is complacent , the Doctor cries out in pain . Malohkeh converses with Commander Restac , wondering if there has been any word from Alaya . When Restac briskly responds in the negative , Malohkeh assures her that it is all right to show some emotion as they are from the same genetic line . Malohkeh begins to decontaminate the Doctor and Nasreen ; again , the Doctor cries out , begging Malohkeh to stop . Because the Doctor is not human , the decontamination process affects him differently — not only does it cause him severe pain , but it removes half of the bacteria keeping him alive . Against Restac ' s wishes , Malohkeh stops the process after seeing an internal scan shows he is not human . Thanking Malohkeh , the Doctor asks if they have any celery . Malohkeh explains the drill threatened the oxygen pockets above the city ; the Doctor is pleased to hear about such technology , but then realises that the impending drill wasn ' t a very nice greeting . The Doctor asks for Restac ' s identity , learning to his annoyance that there is a military . Restac demands to know where the rest of their " invasion force " is . The Doctor tells Restac that the two of them are not an invasion force , revealing that they ' ve come down to negotiate a trade of prisoners : Alaya for the three humans the Silurians took . Restac , however , is less inclined to negotiate , and orders the execution of Nasreen and the Doctor out of spite . On the surface , Tony approaches Alaya for help in curing the venomous sting on his shoulder , promising to release her if she can do something for him . Alaya refuses and amuses herself by having Tony describe what the venom ' s effect feels like . Ambrose eventually learns of Tony ' s injury and Alaya ' s refusal to help . She angrily confronts the Silurian , threatening her with a taser . Alaya encourages her to use it , which she does ; on the second shot , Alaya collapses as Tony and Rory arrive , and she dies in Rory ' s arms . They both become angry with Ambrose because she killed their only bargaining chip to get their loved ones back . Ambrose expresses remorse for what she ' s done . Restac and Malohkeh lead the two prisoners to the city ' s execution chamber , flanked by Silurian warriors . The Doctor explains the nature of the Silurians ' hibernation to Nasreen : centuries before , their astronomers predicted a planet was on a crash course for Earth , so they hibernated below the surface to avoid the catastrophe . The planet was , in fact , the moon coming into alignment . Malohkeh is impressed with the Doctor ' s knowledge of their race , prompting the Doctor to reveal that he ' d previously met another branch . Restac is happy to hear more of her race has survived ; however , the Doctor sadly informs her that humans killed them , reigniting Restac ' s rage . ( Although he keeps his own murdering of Silurians ( and Sea Devils ) a secret . ) Once inside the execution chamber , Mo and Amy appear , brandishing guns they have taken from sleeping Silurian warriors , with the intention of rescuing the Doctor . Restac swiftly disarms Amy , forcing their surrender . The two are added to the procession . When Malohkeh protests , Restac dismisses him . On the surface , Rory and Tony berate Ambrose for what she has done to Alaya . Suddenly , Restac ' s face appears on the screen of a deactivated computer monitor in the church cellar . She has somehow manipulated the monitor to address the humans and negotiate Alaya ' s return . Though the Doctor orders Ambrose to let Rory handle the situation , she steps in and declares she has had enough of the Silurians ' orders . She refuses to return Alaya unless Restac releases her family . Angered , Restac orders the first execution : Amy . The computer monitor goes dark . However , before the Silurian warriors can fire , their leader , Eldane , arrives with Malohkeh and countermands the order . Malohken knew Restac was only acting on bigotry and needed their wiser leader to make the decisions . Eldane tells Restac to " go play soldiers " somewhere else , dismissing her . Now free , the Doctor , realising his chances of negotiating have been reignited , resumes communications with his companions on the surface , ordering them to bring Alaya down via the Silurian transport pods in the mine store room . Reaching the mine , Ambrose encourages Tony to reactivate the drill on a timer in case things go wrong . The Doctor appoints Nasreen and Amy as the ambassadors for humanity and allows them to talk to Eldane . Amy wonders if the Earth is shared in the future , prompting Nasreen to ask what she means . The Doctor reveals that he and Amy travel in time , surprising both Nasreen and Eldane . He then explains time is in flux at this moment , which means they can create a future where humanity and the Silurians live harmony on the surface , rather than have more genocide . Calling the meeting together , the Doctor leaves with Mo to collect Elliot . Malohken brings Mo and the Doctor to the stasis chamber Elliot is in ; he begins shutting it down . The Silurian explains that he didn ' t mean any harm , he just slowed Elliot ' s growth so that he can study how he matures . Malohkeh explains that his family has been studying human evolution through the centuries , but he is the only one awake for the last 300 years . The Doctor expresses his fondness towards a fellow scientist . The boy is released and the Doctor apologises for putting him in harm ' s way . Elliot happily forgives him . The Doctor , Mo and Elliot return to the negotiations , but Malohkeh opts to stay behind to check something . Hearing that cryo - storage has been opened , he rushes to see what is happening . He discovers Restac has awoken more of her warriors . She states that she is protecting them from the apes , clearly showing that she has been consumed by a xenophobia towards humanity . Restac tells Malohkeh that he has done good work , but has no place during war ; she kills him , leaving the others unaware of her growing insanity . Amy , Nasreen and Eldane talk about how the Silurians might be able to live alongside humans . Amy proposes using areas of the Earth uninhabitable to humans ( such as deserts ) as new habitats for the Silurians . However , Nasreen wonders about the resources and population problem that would ensue ; there ' s already 6 billion humans , what happens when the Silurians start reaching that number ? With the promise of a place to live , Eldane insists his race can bring new technology and resources . Amy and Nasreen are pleased to hear there is benefits to sharing the Earth . As the meeting concludes , the Doctor comments on how well things have gone . However , Rory , Tony and Ambrose enter , placing Alaya ' s body on the floor . Appalled , the Doctor demands to know what Rory has left happened while he was away . Ambrose tells the Doctor that she did it . Sighing , the Doctor tells Eldane that he had no idea about this ; Edlande is understanding , knowing both sisters have a bigoted view of humanity and would do anything to ignite a war . Ambrose pleads that she was only trying to protect her family , but it becomes clear that even Elliot and Mo are disgusted with her . Restac returns and cries at the sight of her sister . She wonders why the Doctor insists they trust humans ; Ambrose then reveals that drill is on a timer and that it will be disabled if the Silurians never come to the surface . When Restac learns Ambrose is responsible , she orders the woman ' s immediate execution . The warriors fire at her , but the Doctor steps in to protect her , using the sonic to blow up their guns . The group is forced to flee the room . Eldane leads the Doctor and his friends to the laboratory . They barricade themselves inside and try to think of a way to proceed . Time is running out before the drill reactivates and destroys the Silurian city , but with Restac ' s warriors surrounding them , they cannot return to the surface and turn it off . Restac ' s too blinded by rage to realise she ' ll die . Eldane decides to use an emergency failsafe called toxic fumigation . He will use the controls to release a cloud of toxic gas across the city . The Silurians in suspended animation in their cryochambers will be safe , but those under Restac ' s orders will be killed . The Doctor , with Nasreen ' s reluctant permission , agrees to program an energy surge to destroy the drill and prevent any further threat to the city while using the controls and his sonic screwdriver to deactivate the Silurian force field on the surface . Though the Doctor regrets the failure of compromise , Eldane insists the Earth is not ready for the return of the Silurians yet . With this , the Doctor informs his companions that in a thousand years , the Silurians will return to the surface no matter what and they must spread the word , either religion or rumour ; the Earth must be ready to accept the Silurians . Tony decides to stay behind when he learns the Silurians can cure his wound , which is causing mutation . Nasreen also opts to remain with Tony , thanking the Doctor for helping her fulfill her dream of seeing the Earth . The Doctor ushers his companions to the TARDIS , ordering the Northovers inside and telling them where the medical bay is . However , he is distracted by the sight of a crack opposite the TARDIS ; Amy recognises it instantly . The Doctor is distressed that he doesn ' t understand it , especially when he remembers that Prisoner Zero and the Weeping Angel s seemed to know what it was . Knowing that the cracks were caused by a temporal explosion , he muses that with an explosion , there is shrapnel , and reaches into the crack ; wincing in pain , producing a shard of smoking debris . Before he can take a good look at it , Restac crawls into the room , having let herself be poisoned so she can get her revenge . She aims her weapon at the Doctor , but Rory jumps in the line of fire , taking the hit . Before Restac can fire again , she dies . After a brief conversation with Amy , Rory dies in her arms . The Doctor , seeing Rory has already been surrounded by the time field , forces Amy into the TARDIS , where they watch as Rory is slowly being wrapped in tendrils from sent out of the crack . A devastated Amy reminds the Doctor what he told her after the " Byzantium " : she remembered the Clerics because she is a time traveller . This , however , is her " own " history changing , so it ' s different . He tries to help Amy remember Rory , which he admits is possible if there is no distraction . As Amy remembers Rory , her memories of him begin to fade . Amy tries her best , but the TARDIS has a bumpy landing that breaks her concentration . She forgets all about him . All that remains of Rory is the engagement ring he gave Amy lying on the floor of the TARDIS console room , and the Doctor ' s memories of him ; the ring exists because the inside of the TARDIS exists outside of the normal time - space . The Doctor , Amy , Elliot , Mo and Ambrose rush out of the TARDIS to see the drill explode . Some time later , Ambrose wonders why the Doctor didn ' t leave her to be killed by Restac ; he tells her that and eye - for - an - eye leaves the world blind , and that it ' s never the way . Firmly , the Doctor tells Ambrose to make up for her murdering of Alaya by making sure that Elliot grows up to be the best of humanity , which she had failed to be . The Doctor and Amy return to the TARDIS . Amy stops to wave at her future self on the opposite hill ; for a moment , she believes she saw someone else next to her as well , but quickly forgets about it , reminding the Doctor of Rio . Once she is inside the TARDIS , he remembers the debris he pulled from the crack . It is a scorched blue and white fragment of wood with black lettering . The Doctor holds it against the sign on the TARDIS door , confirming it is a broken piece of the TARDIS exterior . The Doctor worriedly enters the TARDIS . Home video releases . BBC Video - " Doctor Who Series Five - Volume Three " was released on 2 August 2010 ( UK Only ) on DVD and Blu - ray , featuring " Amy ' s Choice " , " The Hungry Earth " and " Cold Blood " .