The Master's line comparing Operation Exodus to being more like a "Genesis of the Cybermen" is a reference to "Genesis of the Daleks", which showed the Fourth Doctor being sent to the creation of the Daleks. Following the success of "Genesis of the Daleks", a story entitled "Genesis of the Cybermen" was planned, but never produced. It is also a play on Operation Exodus and the biblical books of Exodus and Genesis. Perhaps coincidentally, Doctor Who Magazine had previously published a trilogy of stories entitled Exodus/Revelation!/Genesis!, which also featured the Cybermen. Also, Genesis and Revelation (but not Exodus) have been used as titles in the '...of the Daleks' formula.
For the first time in the television series (but far from without precedent across the franchise), the Doctor actually self-identifies using the name "Doctor Who". He has previously been referred to as such in the TV series (examples from across the franchise being far too numerous to list): in The War Machines: Episode 1 (1966), WOTAN says "Doctor Who is required" due to a script mistake; in The Highlanders: Episode 1 (1966), the Second Doctor introduces himself as "Doktor von Wer" (German for "Doctor [of] Who"); in The Underwater Menace: Episode 1 (1967), the Second Doctor signs a note with "Dr. W."; in The Dæmons, the Third Doctor is introduced as "the great wizard Qui Quae Quod" (Latin variations of "Who"); from Doctor Who and the Silurians to The Five Doctors (1983), the Doctor's car Bessie's plate read WHO 1, and in Battlefield it read WHO 7, and in Rose (2005), a website called Doctor Who? asks "Who is Doctor Who?". Although Missy claims that "Doctor Who" is the Doctor's real name, she also explicitly says she calls herself Doctor Who to head off the usual response heard when the Doctor introduces himself and people reply, "Doctor who?". She also states that he chose the name himself, suggesting she means "real name" in the sense of self-designation.
For the story's setting, Steven Moffat conceived of a colony ship where the passengers became trapped for generations following the malfunction of the robotic pilot. This notion was refined through conversations with his son, Joshua, who was studying Physics at university. The younger Moffat had developed an interest in relativistic effects: the way that normal physical laws broke down at speeds approaching that of light, or in the presence of an enormous mass. One associated phenomenon was time dilation, which saw time passing at different rates for different observers, and he noted his surprise that it featured so rarely in popular science-fiction. This discussion prompted Moffat to replace the ship's robotic pilot with a black hole, which would cause time to accelerate on the parts of the vessel that were closest to it. This device would also provide the opportunity to incorporate more recent types of Cybermen.
The eerie institution in which Bill found herself after awakening on Floor 1056 was inspired by Steven Moffat visiting his mother in hospital.
This marks the first appearance of the original design of the Mondasian Cybermen in a televised story since the Cybermen's debut story, "The Tenth Planet" in 1966.