Originally this was meant to be a season premiere, and the start of a season long arc where Superman would have to win back Humanity's trust. However, the executives wanted Timm and Dini to work on Batman Beyond instead, and as such the arc was never produced.
A common concern is that Supergirl is the only one who responds to Kal-El's invasion of Earth. Why aren't Green Lantern, Flash, Steel, Fate, and any number of other super-powered heroes we've seen so far showing up to help?
Much like the Thanagarian invasion on Justice League, most likely Earth's other heroes were each fending off Darkseid's forces in their own neck of the woods. Also, Green Lantern may have been off-planet and Aquaman probably just didn't care.
In the previous episode, Lex Luthor says, "No way he survived that!" after hitting Superman with the kryptonite missile. But in this episode's recap, Luthor says "Nothing could survive that!"
General Hardcastle: To who Superman? You betray us poor earthlings attack us in cold blood, How would you end back our trust rescue a kitten from a tree?
Darkseid: You dare strike me!
Darkseid: A Final gift my wayward son. A fast death, infinitely preferable to the shame of returning to earth. There your legacy would be one of fear and distrust. A pariah desperately chasing a favor of a world, that cursed your name.
Darkseid: I am many things, Kal-El, but here I am God.
Darkseid: Welcome, Kal-El, my son.
How come Supergirl's arm is in a sling when we are shown that she only took a direct hit to the chest?
Superman becomes angry with Dr. Hamilton and chokes him. This later results in the Doctor joining Project Cadmus to defend humanity against the Justice League in Justice League Unlimited.
Tim Daly's final performance as Superman for Timm-produced animated series. George Newbern would take up the mantle for Justice League Unlimited. Although, Daly would return to the role for the 2006 DVD Movie, Brainiac Attacks, and 2009's Superman/Batman: "Public Enemies."
Superman punches Lex for the first time.
Series creator Bruce Timm personally story-boarded the climatic final fight scene with Darkseid to ensure that it would have as much impact as possible.