Supreme Dalek (Prisoner of the Daleks)

A Supreme Dalek directed the Dalek war effort during the Second Dalek War of the 26th century, (PROSE: Prisoner of the Daleks) although it was still subordinate to the Dalek Emperor. (AUDIO: The Dalek Conquests)

Biography
Towards the end of the war, circa the 2580s, the Supreme Dalek was based on Skaro while managing the war. The Daleks privately realised they were losing and enacted a bold strategy intended to prevent an impending defeat. The Supreme Dalek's Temporal Research Team was involved in secret operations on Arkheon, seeking to win the war via time travel by exploiting the Arkheon Threshold to alter human history.

When the Tenth Doctor was captured on Arkheon, the Supreme Dalek was informed. He dispatched the Dalek Inquisitor General, Dalek X, to interrogate him and extract any useful information from his mind via a mind probe. The Doctor was facetious, acting insulted when he learned the Supreme Dalek was not coming to interrogate him himself, but Command Dalek retorted that he would have found an interrogation by the Supreme Dalek preferable to one by Dalek X. The Inquisitor General was totally loyal to the Supreme Dalek and reported only to him, proving to be one of his top commanders.

Ultimately, Dalek X was outwitted and his flagship, the Exterminator, was destroyed by the Doctor on Hurala, along with the Temporal Research Team. The Dalek Fleet was thrown into disarray and the time travel experiments had to be abandoned. Although Dalek X survived the disaster, the Supreme Dalek gave him up for dead. The Doctor warned Dalek X that, in light of his role in the catastrophic reverses suffered by the Daleks, the Supreme was unlikely to be in a forgiving mood if the Inquisitor General ever returned. (PROSE: Prisoner of the Daleks)

Possible identification
The Supreme Dalek never appears in Prisoner of the Daleks and is only talked about. There is scope for this Dalek to be the same individual as one of the Daleks that have appeared in other stories about the Second Dalek War, such as the Gold Dalek in Frontier in Space, the Dalek Supreme in Planet of the Daleks, or one of the Daleks proposing Operation Divide and Conquer to the Dalek Emperor in The Dalek Conquests. However, no concrete distinction has been made in this regard.

Doctor Who and the Planet of the Daleks identifies the black and gold Dalek Supreme from Planet as second-in-command to the Dalek Emperor. This is certainly compatible with the authority of the Supreme Dalek from Prisoner.

However, the two stories are separated by several decades during which the Second Dalek War is fought and much could have changed in the course of the conflict. For example, Nemesis of the Daleks apparently sees the destruction, during the war, of the Emperor Dalek himself! (At least, he is onboard the Death Wheel shortly before it blows up, though his death is not explicitly depicted.)

Like Dalek X, the Supreme Dalek is referred to as a "he" (by the Doctor at least) rather than an "it" like all the standard Daleks. In Planet of the Daleks, the Daleks themselves also refer to the Dalek Supreme from that story as "he".