The Doctor finds himself in an "unholy alliance" with Sec, realizing that a Dalek with a soul is a preferable alternative to a galaxy of genocide. By intentionally interfering with the gamma radiation strike atop the Empire State Building, the Doctor infuses the hybrid army with Time Lord DNA, granting them the freedom of will they were initially denied.
The central conflict arises when Dalek Sec, the leader of the Cult, merges with the human Mr. Diagoras to become a human-Dalek hybrid. Unlike his predecessors, Sec begins to experience "humanity"—feeling regret, compassion, and an appreciation for the "great survivors" of the universe: mankind. [S3E5] Evolution of the Daleks
The Unholy Alliance: Identity and Ideology in Evolution of the Daleks I. Introduction The Doctor finds himself in an "unholy alliance"
The remaining members of the Cult—Caan, Jast, and Thay—represent the traditional Dalek dogma of "purity". Their eventual mutiny against Sec highlights the self-destructive nature of Dalek philosophy. To these Daleks, any deviation from their original form is a "sickness," even if that deviation is the only path to avoiding extinction. Diagoras to become a human-Dalek hybrid
"Evolution of the Daleks" concludes the two-part story set in 1930s New York, where the Tenth Doctor faces a weakened but desperate Cult of Skaro. While the episode is often noted for its pulpy sci-fi elements—including the "Pig-Men" and the iconic backdrop of the Empire State Building—its true substance lies in the psychological fracture of the Dalek race. The episode serves as a character study of Dalek Sec, who attempts the unthinkable: the integration of human emotion into the Dalek genome. II. The Hybridization of Dalek Sec