A possible link was made between the Supergirl show and the Man of Steel (2013) movie when Wynn mentions that Superman killed Zod.
Alex mentions to Sam that before the DEO, she was a doctor in Seattle. This was a nod to Chyler's previous role as Dr Lexi Grey in Grey's Anatomy. Creator Greg Berlanti put in that line and Chyler "didn't even get it right away" until it was the table read and she said it out loud and then realised and said it was "clever." Greg told her "that was a little wink for you."
Near episode's end, James doesn't object when Lena calls him "Jimmy". In the series premiere, he tells Kara that he prefers "James", and that the nickname is reserved for his mother and Superman.
A new mystery about Samantha/Reign rises when Alex is able to stick the needle in Samantha's arm to draw blood with no problem.
Mon-El mentions getting the idea to use Lilian's drone against her from a battle with Computo. In the comics, Computo was created by Brainiac-5.