The eight faces in The Brain of Morbius, which appeared to be faces of the Doctor from before the first episode of Doctor Who, were an in-joke, faces of Doctor Who showrunners. Shortly after The Brain of Morbius, in The Deadly Assassin (1976), there was dialog establishing Time Lords have a twelve-regeneration limit, "regeneration" referring to the process (though Time Lords do also use the word "regeneration" as a synonym for "incarnation"), so twelve regenerations means a total of thirteen faces. Later episodes established that the capacity to regenerate more than the standard twelve times can be granted or taken away by the Time Lord authorities. One popular rationalization in continuity discourse since The Brain of Morbius for the Doctor's extra faces is that those were actually Morbius' faces (the Doctor's dialog in the previous panel alludes to this interpretation), which could be argued from the way the scene is edited, but is inconsistent with Sarah Jane's reactions while watching them. Another popular rationale is that the Doctor had a previous regeneration cycle. The Hero of Three Faces incorporates this. However the incarnation first appearing in Doctor Who, the first incarnation of the second cycle, remains "the first Doctor" (e.g., The Three Doctors, 1973) because it was upon being granted a second regeneration cycle that the Doctor adopted the title to the exclusion of his given name.

The reason this cartoon was removed from The Hero of Three Faces continuity is that the Doctor Who episode The Timeless Children (2020) created in screen continuity a different scenario for the Doctor having previous lives than the first onscreen Doctor, one that the Doctor had not been aware of. This cartoon has been replaced in Three Faces continuity by another one with the same art for the first two panels.