Reference is made to Jeremiah Danvers in this episode. It was previously believed that Jeremiah had been dead for ten years, but "Manhunter" revealed that he might in fact be a live and is a prisoner of Project Cadmus.
Reference is made to Working Girl in this episode, which is a 1998 romantic comedy directed by Mike Nichols. Coincidentally, Working Girl stars Harrison Ford, who is the husband of Supergirl actress Calista Flockhart. This is the second time that Working Girl has been referenced in the series, and is the third time that a reference has been made to Harrison Ford.
Supergirl can be clearly seen wearing earrings (not clip-ons) in this episode, which should be impossible. The only item that could pierce her skin is Kryptonite, which would kill her. Or at the very least, give her a very nasty ear infection.
Alex tells Kara that she would be adrift in space with no means of thrust if she hurls Fort Rozz off planet. Supergirl could have simply used her heat vision on the fort to give her the momentum to slip back into Earth's atmosphere.
Although Alex Danvers is very intelligent, it is unlikely that she would have been able to successfully pilot Kara's Kryptonian rocket. It is also left unexplained how she got her back to Earth as there is only room in the pod for a pilot.
It is never explained why Superman does not awaken after the effect of the Myriad wave wears off. This is a plot contrivance to keep him out of the episode so that Kara can save the day on her own.
J'onn J'onzz is a very intelligent and strategically minded being. It is inconceivable that he would not have brought some Kryptonite weaponry with him to help Kara against Non. But then, we wouldn't have gotten that cool heat-vision power struggle scene.
Why did Indigo suddenly shut down? She's been deconstructed in the past and instantly reconstituted herself. J'onn tearing her in half should have only stalled her for but a moment.
At the end of the episode, a Kryptonian rocket crash lands in Midvale. Supergirl opens the pod and exclaims, "Oh my God", implying that she recognizes its occupant. So who is in the pod, and what does this mean for Supergirl?
Why did Superman decide to catch up on a little kip rather than helping Kara save the world? He should have been the first to awaken after Kara's broadcast message of hope.
Will Lucy Lane still have a place at the DEO?. Now that J'onn is large and in charge again, he implied that he would want to continue to have Lucy work with them, but nothing is indicated for certain.
What's that wily ole Maxwell Lord doing with the Omegahedron? You know... that boundless Kryptonian energy source that was used to fuel Myriad. It appears as if he is giving it to Sam Lane, but they both seem to be keeping this exchange on the DL.