The Doctor Dances

Continuing from the cliffhanger of "The Empty Child", the Doctor orders the beings to go back to their room - thus causing them to return to their beds and, unbeknownst to him, saving Nancy from her brother Jamie. The Doctor, Rose and Jack go to Jamie's room where the Doctor realises that the being that was Jamie is still learning what it can do and soon, will be too powerful to stop. The Doctor turns to discover Jamie waiting in the doorway. Escaping from Jamie and the other creatures (under Jamie's control), they end up trapped in a room. Jack teleports back to his ship and uses Glenn Miller's "Moonlight Serenade" to prevent Jamie using the radio to track the Doctor and Rose. Challenged by Rose to dance while they wait, the Doctor accepts but is interrupted when they are transported to Jack's Chula ship. The Doctor uses the ship's nanogenes to heal a wound while Jack explains that he went renegade on the Time Agency when they stole two years of his memories.
Meanwhile, Nancy is briefly caught by the family returning home. Managing to blackmail her way free, she returns to the railyard to tell the other children they are not safe while they are with her. Telling them of her plan to head to the bomb site, Nancy does so but is quickly captured. Despite her pleas, she is left with a guard who subsequently transforms into a gas mask-wearing zombie. The Doctor, Rose, and Jack arrive at the bomb site and realise that the contagion is now airborne as the soldiers there begin to transform. Freeing Nancy, the Doctor investigates the 'bomb' which is actually the empty shell of a Chula medical transport. Realising that the ship also contained nanogenes, the Doctor deduces that the transformations are caused by nanogenes who have used Jamie's dead body in a gas mask as a template for all humans. As they attempt to open the transport, it transmits a "call to arms" instructing all the altered humans to come to battle; as the Chula were a warrior race, the nanogenes have given the transformed beings enhanced abilities. The altered people from the hospital arrive at the railway station but stay at a distance, and the Doctor realizes that since Jamie was the template, it is his mind that drives them; his looking for his "mummy". A distraught Nancy claims that the situation is all her fault, and as the Doctor tries to reassure her, he notes her grief and deduces that she is not, as she appears, a fourteen year old girl and that Jamie was not her brother but her son.
Jamie heads through the gate and approaches Nancy, still asking if she is his mummy. The Doctor instructs Nancy to tell Jamie the truth, and she tearfully does so, embracing her son. The nanogene cloud gathers around the two, and are able to identify Nancy's DNA as being that of a parent, and they reverse the transformation on Jamie, restoring him to life. The Doctor then scatters the nanogenes over the assembled zombies and they are all restored, as he proclaims that "Just this once, everybody lives!" As the German bomb falls onto the site, Jack uses his ship to capture it and remove it to the far reaches of space; the Doctor sets the medical transport to explode, thus destroying the technology and matching the historical records of an explosion at the site. Aboard his ship, Jack finds he cannot stop the bomb from exploding or abandon his ship, but is rescued when the TARDIS materializes at the rear of his ship. Joining the TARDIS crew, Jack watches as the Doctor and Rose dance in celebration.