The Cadmus data files names contain at least three nods to the comics:
- "Zarathustra" is a reference to the codename to the British government program that created Miracleman.
- "Multiverse" is a DC Comics continuity construct.
- "Flashpoint - 23" refers to the next episode, which is the 23rd episode of Justice League Unlimited.
Here, it is revealed General Eiling is Captain Atom's former commanding officer in the Air Force. In DC Comics, General Eiling is the original antagonist of Captain Atom. First he blackmails the then-Captain Nathaniel Adam into participating in the military experiment that transforms him into living energy, then marries Adam's wife and raises her children as his own.
The Question's interrogation scene was purported to be carried out by Dr. Hugo Strange. According to Dwayne McDuffie, Strange's cameo in "The Doomsday Sanction" was a set-up for this scene, but due to the Bat-Embargo he could no longer be used and was replaced by Dr. Moon.
Superman and Captain Atom defeat Mantis in the "Plastino Street Station", an homage to Al Plastino, the Silver Age Superman comic artist.
During the Question's speech to Lex Luthor, he says, "A is A," an allusion to Ayn Rand's philosophy of Objectivism. Steve Ditko, the Question's creator, was a noted adherent to Objectivism. Ditko also created the similar character Mr. A, who was much more explicitly Objectivist, and whose name was a reference to "A is A."