The episode was previously titled "Elseworlds: Hour Three".
Barry breaks the fourth wall in this episode; he says "this has gotta be the craziest thing you've heard in the past three hours"; a reference to the fact that the Elseworlds crossover is split into three hour-long installments.
This is the first Supergirl episode to include Lois Lane, as she was previously only mentioned in earlier seasons.
The opening monologue in this episode was narrated by John Deegan. But for the last line, he says it after transforming into Superman.
Near the end, Deegan's face is shown disfigured in black and white almost like a skeleton, similar to his comic book counterpart's appearance.
After The Monitor tells Barry and Oliver that Earth-1 might have a chance to prevent the crisis, Barry says "If that's supposed to be a pep talk, I've had better." This is a reference to the many incidents on The Flash when Barry was given a pep-talk that helped him solve a problem.
When John Deegan becomes Superman and rules the Earth, this is a reference to the plot of the video game Injustice: Gods Among Us where Superman is a tyrant that rules the Earth.
When Deegan fought Superman in a building, a civilian calls him "Bizarro". This is a nod to Bizarro, who is female in the Arrowverse.
Kara correctly guesses that Lois and Clark are having a baby, a reference to Jonathan Samuel Kent, who first appeared in DC Comics' Convergence event in the miniseries Convergence: Superman #2 (July 2015). Jonathan is the biological firstborn son of Superman/Clark Kent and Lois Lane and is half Kryptonian/human.
The fact Superman is taking Lois to Argo in order to safely carry the child (with kicking in the womb being mentioned a specific risk) is a callback to longstanding fan speculation over the logistics - and even impossibility - of superpowered Clark and human Lois having a child or simply a sexual relationship. The best known example of this is science fiction writer Larry Niven's classic essay, "Man of Steel, Woman of Kleenex".
While in the Fortress of Solitude, Superman presses a piece of coal into a diamond to put it in a ring and propose to Lois Lane, resembling Smallville's 100th episode ("Reckoning"), when Clark Kent did the same to propose to Lana Lang. The aforementioned scene itself is a reference to Superman III, when Superman presses a piece of coal to give Lana Lang a ring after she tells him she has to sell hers.
Superman says to John Deegan as Superman, "doctor, can I have a word?", a similar quote to Superman II, when he says to Zod, "General, would you care to step outside?"
At the end of this episode, Roger Hayden says "Worlds will live. Worlds will die. And the universe will never be the same." Psycho Pirate said the exact same thing in the comic book crossover Crisis on Infinite Earths.
Flash and Supergirl dying in Superman's vision of the future is a reference to the original Crisis on Infinite Earths story-line, where both heroes sacrifice their lives to save the universe.
Barry and Oliver having a drink in the ending scene is a nod to the ending of "Invasion!".
When Barry asks Oliver to hug him, he rudely responds "no" as he made him hug him twice, referring to the episodes, "Legends of Yesterday" and "Invasion!".
In trying to track down the Cisco Ramon of the new reality, Barry tells Oliver that the last alternate version of Cisco he met wasn't very helpful, likely a reference to the version of Cisco that existed in the Flashpoint timeline, a business magnate with very little interest in metahumans and crime-fighting.
Lois reveals to Clark that she and him are expecting their first child together. In reality, Elizabeth Tulloch was six months pregnant while shooting the Elseworlds crossover at the time.