The Rebel Flesh ( TV story ) The Rebel Flesh was the fifth story of the sixth series of " Doctor Who " . Like many previous stories , it saw the Doctor duplicated . It was the second time that the Eleventh Doctor was copied following " The Eleventh Hour " . It introduced the Flesh concept to the Whoniverse and showed the Doctor had an ulterior motive for wanting to get rid of Amy and Rory for a while . It marks yet another time the Doctor has tried to make peaceful negotiations with humans and another species , but failed due to one side taking a life . This previously happened in " Cold Blood " of Series 5 . It was notable for the first use of motion control camera s since " The Mysterious Planet " . It contained the first instance of motion control use on actors rather than inanimate models in " Doctor Who " history . Synopsis . The Eleventh Doctor , Amy Pond and Rory Williams visit an acid - mining factory . A solar storm hits the factory , turning the workers ' ganger s into self - aware individuals . The Doctor must mediate between the original workers and their rebellious gangers . Plot . On an island , factory workers Jennifer , Buzzer , and Jimmy move through the monastery . In a small chamber containing one large , circular vat filled with acid , they wear acid suits to protect themselves . Jennifer is perplexed by the acid readings . Buzzer teases her . In response , she hits his leg , and he falls into the vat . Jennifer and Jimmy seem more concerned about the loss of the acid suit . As they leave , Buzzer enters the hallway they ' ve begun walking down and angrily confronts them . He is still seen melting in the vat of acid . In the TARDIS , the Eleventh Doctor scans Amy for pregnancy and continues to get uncertain readings . At the same time , Amy and Rory are playing darts while listening to music being played from the console . The Doctor asks Amy and Rory if they ' d like to go for fish and chips while he takes care of something else . Amy objects to being dropped off . Before this issue can be resolved , the TARDIS is hit by a solar tsunami . The TARDIS rocks violently as the Doctor tries steering to safety ; however , he gives up and yells for Amy and Rory to take cover as they ' re about to land . With a soft thud , the TARDIS lands and the Doctor heads outside to see where they are . They ' re arrived at a 13th century monastery ; Amy thinks this means they ' re in the Medieval Era . However , Rory tells her that it ' s not likely as he can hear Dusty Springfield playing near by . Rory notes his mother is a fan of Dusty ' s music , to which the Doctor says he is too . They investigate the interior , not knowing someone is watching them . Seeing piping , the Doctor scans it with the sonic screwdriver , noting that it has a ceramic interior , meaning something corrosive is being pumped off the island . Rory touches a wet spot and pulls his hand back in pain . The Doctor tells him it ' s old acid ; Rory ' s lucky it wasn ' t fresh , or his hand would have been dissolved . The monastery has been modified into a 22nd century factory for mining acid . An alarm goes off and the Doctor notices a reading on the sonic , telling Amy and Rory that " almost people " are coming . Searching for these people , the trio end up in a chamber where they spot five harnesses . Four are occupied by sleeping workers . Amy wonders if they ' re prisoners or meditating ; the Doctor tells her it falls into the " or what " category . The factory ' s " security " quickly surrounds them and the time travel lers realise they are exact doubles of the people sleeping in the harnesses . The foreman , Miranda Cleaves , tells the trio that unless they work for Morpeth Jetsan , they ' re in a lot of trouble . Brandishing the psychic paper , the Doctor claims to have come from the new meteorological department ; he warns them that a solar flare — bigger than the one they ' ve just survived — is on its way . They ' re all in danger . However , Cleaves is more concerned with doing their jobs than the lives of her workers . The Doctor requests to see her " critical system . " Cleaves leads the Doctor , Amy and Rory to a vat of Flesh — fully programmable matter which can replicate any living organism . All of the workers in the room , apart from Jennifer , are Flesh " Ganger s , " controlled by the real people who are sleeping in the harnesses . The site is far too dangerous , and they were losing workers every week ; therefore , the military commissioned the creation of the Gangers , who could mine the site and interact with the acid without putting anyone in danger . The Doctor is concerned by their low opinion of the Flesh , but intrigued by its function ; he scans it with the sonic screwdriver and reaches out to touch it . He grimaces in pain and says that it felt like , while he was scanning it , it was scanning him . Jennifer is ordered to her harness by Cleaves ; a small amount of Flesh pours into a tub attached to it . Eyes and a mouth form as the Flesh compresses into Jennifer ' s shape and colour begins filling in . After Jennifer ' s Ganger emerges , the Doctor jokes , " I see why you keep it in a church ; the miracle of life . " The Doctor reminds Cleaves of the impending solar flare , but she refuses to allow her team to leave the island . The Doctor asks for the location of the security systems , being informed by Jennifer where they are . Investigating with Amy and Rory , the Doctor notes that the factory runs on solar energy ; when the wave hits , there will be a debilitating power surge . " I ' ve got to get to the cockerel before all Hell breaks lose . I never thought I ' d get to say that again . " the Doctor laughs , heading to the roof to the weathervane . However , despite his best efforts , the Doctor arrives too late and is knocked unconscious , falling to the ground as the solar storm hits . The acid pipes burst and leak everywhere , eventually causing the TARDIS to sink below ground . As the power surges , the Gangers flicker between their full human forms and semi - Flesh forms . The Doctor awakes to see the weathervane gone and its stump smoking . Going off in search of the others , he finds Cleaves , who is deeply shaken and concerned for her team . They move back into the monastery , with the Doctor asking Cleaves how long they ' d been unconscious ; when she replies a few minutes , he insists that it has been at least an hour , and that a lot could happen in an hour . Amy and Rory awake on the floor of the Flesh room and return to the harness chamber , where they find the rest of the team shaken after the power surge . Jennifer is in a state of shock , and Rory comforts her . The Doctor and Cleaves eventually join them . Cleaves informs the group that the Gangers should have melted into their pure Flesh forms , but the Doctor is uncertain — especially as Jimmy ' s records start to play throughout the monastery . It seems that the Gangers are controlling themselves now . The group runs to the dining hall , which has been ransacked ; the Doctor explains that the Gangers were merely searching for confirmation of their identities . The group has trouble accepting this and believe themselves to be in danger , with Buzzer citing previously recorded cases of Gangers going crazy ; however , the Doctor shrugs this suggestion off . Seeing a house of cards Buzzer says was a trick taught to him by his grandfather , the Doctor explains that Buzzer ' s Ganger was taught by his grandfather as well ; they have the entire identities of who controlled them in their heads . The Doctor tells everyone that they ' ve willingly bequeathed their lives to their doubles ; they are dealing with the miracle of life , not a mess that needs to be mopped up . Jennifer feels ill and rushes to the toilets , closely followed by Rory to keep her protected from crazed Gangers . In the toilets , Jennifer vomits up Flesh while Rory has his back turned ; terrified to realise that she ' s a ganger , she runs into one of the cubicles . As Rory steps in front of the sink and spots the Flesh , Jennifer ' s arm punches through the door of the cubicle and narrowly misses hitting Rory in the face , demonstrating tremendous elastic ability . Her neck also extends through the hole in the door , and she screams , " Let us live ! " as Rory runs out of the room . In the dining hall , the Doctor heats up a plate of food as Jimmy suggests arming themselves against the Gangers . The Doctor wonders if Jimmy is a violent man ; when Jimmy replies in the negative , the Doctor explains that there is no reason to assume his ganger will be . The Doctor hands Cleaves the hot plate , though she doesn ' t react to this until he mentions that it is hot , at which point she drops it . Confused as to why she didn ' t feel the heat before , the Doctor calmly explains that her nerve endings haven ' t finished attaching yet , but that she ' ll stabilise soon enough . Cleaves turns away ; when she turns back , she reveals her Flesh form . The workers demand to know where the real one is , but Cleaves runs out screaming . Amy reminds the Doctor that Rory is Jennifer , who was out of her harness , The Doctor , Amy and Dickens run after Rory and Jennifer , finding the aftermath of Jennifer ' s brief mental snapping . Recalling that the Doctor called the Gangers early technology , Dickens wonders why he ' s really there . The Doctor gives a look towards Amy before insisting that the Gangers aren ' t violent , but scared and angry , and he needs to talk to them if he is going to fix what has happened . They continue through the monastery , but find many of the corridors blocked by leaking acid puddles . The Doctor proposes going to fetch the TARDIS and rushes off ; Amy also goes off on her own to search for Rory . Jimmy returns to the dining hall and sends Buzzer and Dicken off to retrieve the acid suits . Rory finds Jennifer ' s ganger in the locker room ; she insists that she is Jennifer Lucas , not a mere factory part . Jennifer tells Rory about a memory of a time she was lost as a child and imagined and stronger version of herself as comfort . She takes offence when he asks her where the real Jennifer is , and takes on full human form while yelling that she is just as real as the " other " Jennifer . Rory comforts her , accepting her and earning her trust . On his way to fetch the TARDIS , the Doctor returns to the vat of Flesh and scans it once more before leaving . The tub fills with Flesh , and slowly , a mouth takes shape in the liquid , whispering , " Trust me . " Upon reaching the TARDIS , the Doctor is disappointed to find that it has almost completely sunk below ground ; additionally , the nearby acid melts through his shoes , forcing him to abandon them and return to the monastery . Meanwhile , all of the Gangers — apart from Jennifer — have gathered in the acid room with the acid suits . While searching , Amy is horrified to see the eye - patch woman yet again . Not long afterwards , Rory and Jennifer ' s ganger discover her , and they are all joined by Buzzer and Dicken . The two factory workers are pleased to have found Jennifer , but Amy is quick to inform them that this is her ganger . Rory quickly becomes defensive , shouting that no one will touch her . The Doctor , meanwhile , has discovered the Gangers hiding out in the acid room . He tells them that they should try cooperating with the originals , as a fight never ends well for anyone . The Doctor leads them , fully formed , back to the hall ; he asks them to try keeping their appearances as it will make them less scary . They are observed from afar by a contemptuous Miranda Cleaves , who has been hiding out ever since the solar storm . Feeling like she ' s been watched , the Cleaves ganger turns her head , only to see no - one there . They return to the dining hall , where Jimmy , Buzzer , and Dicken interrogate Jennifer ' s ganger about what she has done to the " real " Jennifer ; Amy insists that they should do nothing until the Doctor arrives . And he does so right at the end of her sentence , followed by the Gangers . The Doctor requests replacement shoes and reminds everyone that the Gangers are truly alive ; that destroying them is murder . Jimmy expresses some disdain until his ganger reveals his shared memories of his son ' s birth ; they appear to reach some sort of unspoken truce , even volunteering to go and find Jennifer and Cleaves together . However , before they can depart , the real Cleaves storms the room , brandishing a probe ; Cleaves ' Ganger explains she has a complex that makes her always want to be in charge even when she doesn ' t know what the hell is going on . Cleaves tries killing her double , but Buzzer ' s gets in the way to wrestle the probe from her . Buzzer is zapped and drops dead . The Doctor is furious ; Buzzer ' s ganger had a human heart , and Miranda stopped it . Having witnessed Buzzer ' s murder , Jennifer ' s ganger wrongfully loses her faith in Rory , concluding humans can ' t be trusted ; when Cleaves turns on her with the probe , Rory jumps on her , wrestling it away from her as the Gangers flee , terrified . The Doctor snaps at Cleaves for ruining their chances of working together , prompting Cleaves to arrogantly respond that it ' s " us or them . " Returning to the acid room , Jennifer ' s ganger repeats this — " us or them . " Sensing that the Gangers will launch an attack as retribution for Buzzer ' s death , the Doctor suggests hiding out in the monastery ' s most secure room — the chapel , which happens to contain the Flesh vat . The real Jennifer searches for Rory , but is met with a sneak attack from above by her Ganger . Rory stops running toward the chapel when he hears Jennifer scream out . Despite Amy ' s protests , Rory separates himself from the group and goes off in search of Jennifer . As the Gangers advance on the chapel , the Doctor and his companions barricade themselves inside ; however , the Doctor is quick to sense someone else ' s presence in the room and refuses to focus on the situation at hand . As Amy lectures him , the Doctor ' s voice rings out from the shadows . A semi - Flesh ganger of the Doctor steps into the light , adjusting his bow - tie . " Trust me , " he says . " I ' m the Doctor . " Home video releases . This story was released as Series 6 , Part 1 with " The Impossible Astronaut " , " Day of the Moon " , " The Curse of the Black Spot " , " The Doctor ' s Wife " , " The Almost People " and " A Good Man Goes to War " on 11 July 2011 . The episode was later released in " The Complete Series 6 " , which included the first and second half of the series , was released on DVD and Blu - ray on the 21 November 2011 .