The Choice ( comic story ) The Choice was the eleventh issue of " Prisoners of Time " , and featured the Eleventh Doctor and his companion Clara Oswald . Publisher ' s summary . Our yearlong celebration of " Doctor Who " s 50th anniversary continues ! Geronimo ! The Eleventh Doctor joins the fray in this issue of a 12 - part epic adventure featuring all 11 incarnations of the Doctor . Now that the Doctor has uncovered the true identity of his latest adversary , he must track him through time and space for a final confrontation ! Plot . The Eleventh Doctor and Clara Oswald have just ended a civil war among a race of people called the Frogmen , having told them that Fratalog was the rightful king . The Doctor then says " When I say ' Duck ! ' , I really mean , ' Duck ! ' . However , before anything else can happen a powerful blast of energy knocks both of them unconscious . The Doctor comes round just in time to see Adam Mitchell teleport away with an unconscious Clara in his arms . He heads back to the TARDIS and goes to all the places in which Adam kidnapped his other companions , just after the kidnappings took place , where he attempts to gain information from people who were there , including Agent Paul and the Judoon . But he finds nothing of use , and realises that rather than delving into his own past , he needs to look at Adam ' s . The Doctor breaks into a library , and finds a room where Adam has pinned up pictures of his past incarnations and companions , including a large red cross over the picture of his ninth incarnation . Feeling guilty about what his actions drove Adam to do , he decides to head back to Henry Van Statten ' s Vault in Utah , where he first met Adam , hoping to find some sort of trace he can use to track him down . However , he discovers that Adam has taken every last bit of alien technology that was in there . He breaks into Adam ' s lab , where he finds the Time Agent whom Adam had captured on the floor , " frozen in time . " He releases the Agent , named Neal Shaw , who tells him that he had been awake the whole time and had been forced to wait for months as Adam experimented on him . He gives the Doctor a tracker that will help him find his vortex manipulator ( that Adam had stolen ) and asks to come with the Doctor . The Doctor declines , saying that he would not put any more innocent people in between him and Mitchell . The tracker brings him to a giant fortress in the Time Vortex , which the Doctor enters , calling out for Adam . Adam greets him with a gun , which he uses to paralyze him . He awakes later to see Adam , who tells him that he treats all companion s like he had treated him : with no care for what happens to them afterwards . After some time , enters , scarred , having survived the attack by Aerolith after being tortured for decades and barely escaping alive . Adam reveals that he discovered the Master on his hunt for other people who wanted to " make [ the Doctor ] suffer . " The Doctors warns Adam of the evil of the Master , and of the thousands of lives he had ended to call himself " king of the universe . " The Master laughs the Doctor ' s words off as lies , and instructs Adam to continue with the plan . Adam leads the Doctor and the Master into a large room , where all of the Doctor ' s companions sit in tubes along the walls , even the ones he had not seen captured . Adam holds a remote , one which will kill every companion in the chambers when he presses the button . He tells the Doctor that all of his companions dying might destroy the universe as all of the Doctor ' s history is rewritten , but as they are in limbo they will not be affected and Adam does not care . He tells the Doctor to choose one companion to save , and the rest will die . References . " to be added "