Human Dalek Sec wants humans prepared for hybridization, and then reveals that he can feel humanity. The Doctor intervenes and uses a radio to send out sonic waves that cause Sec pain, with the Daleks protecting him. The prisoners manage to escape from the lair. Two Daleks discuss their doubts about Sec’s methods and plans.

Back at the Hooverville camp, the Pig Slaves attack the settlers to reap more bodies, with two flying Daleks backing them up. They demand surrender from the humans. Solomon addresses the Daleks, with Sec admiring his courage via a visual link. Solomon puts down his gun and tries to reason with the invaders. However, he is exterminated much to Sec’s shock.

The Doctor offers himself to the Daleks, but Sec orders them to keep him alive. The Dalek struggles to obey, craving the glory of killing their greatest foe. The Time Lord is taken to Sec, but slips Martha his psychic paper.

Sec, when asked why he saved the enemy, explains that The Doctor is a genius who might be able to save the Dalek race. Sec tells Doctor the deaths - especially Solomon’s - were wrong. He then shows him that a thousand human bodies are stored for the purpose of turning them into a new race of Human Daleks, their minds wiped and near to death. Their minds will be filled with Dalek ideas. To activate them they need the energy from a solar flare that will strike the Dalekenium panels at the top of the Empire State Building.

Martha works out that The Doctor wants her to use the paper to infiltrate the Empire State Building, which she does so with Jack and Tallulah. They check the architectural plans and notice a recent change at the top.

Sec argues with the Daleks about their purpose, saying they must change otherwise they deserve extinction. The Doctor is asked to help construct the new friendlier race and transport them to another planet using his Tardis. Laszlo also learns from the Time Lord that his pig transformation cannot be changed.

In the basement, the new race is being prepared and the bodies are fed the genes in advance of the solar flare. The Daleks overide the gene feed, declaring both Sec and the Doctor enemies and restrain them. They pump the bodies with 100% Dalek genes.

Laszlo helps the Doctor to escape and they head for the roof to dismantle the Dalekenium. However, the pig slaves are sent to thwart his efforts. Jack, Martha, Tallulah and a fatigued Laszlo prepare to fend off the pig slaves, with the medical student hatching a plan to conduct a bolt of lightning using metal poles to fend off the pigs.

The Doctor drops sonic screwdriver on the roof and is unable to remove the Dalek panels. He clings onto the metal conductor as the flare hits, with the energy passing through him to the basement. The human Dalek army awakens.

Martha’s plan works and the slaves are killed, although she feels remorse for her actions. The Human Daleks are told to assume battle positions, take the Dalek guns and conquer Manhattan - then the world.

The Doctor and his companions head to theatre, using his sonic screwdriver to alert the Daleks to his presence. The Human Daleks then arrive on the scene and surround them. On stage, two Daleks appear accompanied by Sec crawling in chains.

Sec is exterminated after begging his former inferiors to spare The Doctor. Back in the basement , the remaining Dalek notices the human exterminators show increasing signs of serotonin. They refuse to obey orders to kill, questioning them. The Doctor explains that the army has absorbedTime Lord DNA through the lightning strike passing through him. The Daleks open fire on the hybrids - who fire back. Both Daleks are ultimately destroyed. The remaining Dalek self destructs the surviving human Daleks, much to The Doctor’s anger as he says it was genocide.

The Doctor confronts Delak Caan - saying he might be willing to show him some compassion as he is the last in his race and he doesn’t want another genocide. Caan uses an Emergency Temporal Shift to escape.

Laszlo seems to be nearing the end of his life span, but The Doctor intervenes and saves his life, although he can’t change his looks.

The Doctor and Martha bid farewell to the others and leave New York, with the time Lord admitting that one day he will encounter the sole surviving Dalek again.