After the creation of the hybrid Dalek-human, the Tenth Doctor confronts the Cult of Skaro and helps Martha and Frank escape. As Dalek Sec begins experiencing emotions Dalek Caan and Dalek Jast discuss their lack of confidence in him, hinting that a change of command may be needed. The Doctor and Martha return to Hooverville, which is attacked by the Daleks. Although Solomon is killed Dalek Sec orders the Doctor to be brought to him alive.
At the Dalek lab at the Empire State Building, the Doctor learns that the Daleks are planning to combine their DNA with humans and create more hybrids. The process requires more energy than can be generated with the technology of 1930, so the Daleks plan to use gamma radiation from a solar flare. The Doctor agrees to help once he realises that the human subjects are already brain dead and cannot be saved otherwise. He also offers to take the new hybrids and the Daleks to a new planet in the TARDIS so they can start over, in which Dalek Sec agrees. Daleks Caan, Jast, and Thay stage a mutiny, chaining up Dalek Sec and declaring him a traitor. The Daleks then decide to replace the human DNA completely with their own. The Doctor regroups with Martha, who has analysed the building plans with Frank. Martha tells the Doctor he must remove the Dalekanium panels on the mast of the building to stop the energy collection. The Doctor drops his sonic screwdriver before finishing in time and ends up holding the mast as the strike hits. The energy flows down the building, awakening the new hybrids.
The Doctor returns to the theatre with the human-Dalek army following them in the sewers. In the theatre, the Doctor pleads with Daleks Thay and Jast to listen to Dalek Sec and let him help. They refuse, attempting to kill the Doctor but Sec steps in between and sacrifices himself. The Daleks order their army to kill the Doctor, but find that the humans are questioning orders. By exposing himself to the gamma strike, the Doctor caused some of his Time Lord DNA to transfer to the human shells. The army turn on Thay and Jast, killing them. Dalek Caan activates a termination sequence to kill the rest of the army. Upset by this act of genocide, the Doctor returns to the Dalek lab to face Caan, but Caan escapes once again via emergency temporal shift.