Originally, this two-parter was supposed to be the first episodes of this season, and Superman would spend most of which winning back the people's trust. However, Bruce Timm and Paul Dini were asked to produce Batman Beyond, so this ended up being the finale for a short-lived season. The arc of Superman making amends was played out in Justice League.
Superman punches Lex and Darkseid for the first time.
Bruce Timm, series creator, personally story-boarded the final fight scene between Superman and Darkseid to ensure that it would have as much impact as possible.
Granny Goodness's line "This time I won't leave you wits enough to pick your..." was originally intended to be "This time I won't leave you wits enough to wipe your...", but Bruce Timm had to change it.
Superman: So it ends like this.
Lex Luthor: Don't think of it as an end, Superman. My biotech people will spend years studying you carcass. I'm certain it will be a most profitable endeavor.
Superman: Lois! What are you doing in here?!
Lois: Have you ever tried to get a story out of the military? I figured it'd be easier to go straight to the source.
Superman: It was Darkseid. He stripped away my memory, turned me loose to destroy everything I've ever loved. First the invasion of Earth, then the murder of Dan Turpin, now Supergirl's life is hanging by a thread and I'm an outcast. Darkseid is responsible for all of it.
Lois: What are you gonna do?
Superman: Settle it. Once and for all.
You used me.
I told you once, Superman, if you would not be my knight, you would be my pawn.
I see you're a man of your word.
I am many things, Kal-El. You couldn't begin to imagine half of them, but for now I shall take the role of executioner.
Superman: (punches Darkseid)
That's for Dan Turpin!
The good man you murdered!
Had I known one human's death would pained you so, I would have killed more. And kill more I shall. Carry that agony with you to oblivion, Superman.
I am many things, Kal-El, but here I am God.
Lois: Don't listen to them.
Superman: No. They're right. I did lose control and it scares me. If I can't trust myself, how can I win back the trust of an entire planet?
Lois: (kisses him) One person at a time.