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Brainiac's ship is a new version of the same one in which he first arrived on Earth in Stolen Memories (1996).
Hawkgirl's account of how she ended up on Earth - inadvertently being transported and stranded there by experimental technology - is actually the comics' original story for J'onn J'onzz's arrival from Mars.
When Batman uses a boom tube for the first time, he sarcastically remarks to Wonder Woman "that was pleasant". In the Batman Beyond (1999) episode The Call: Part 1 (2000), old Bruce Wayne mentions to Batman (Terry McGinnis) that he always hated the boom tubes.
Superman and Wonder Woman are now drawn without cheekbone lines since a lot of fans disliked them.
Darksied was given a subtle more "Kirbyesque" redesign from his appearances in Superman: The Animated Series (1996) to closer resemble Jack Kirby's artwork.
When Batman is lecturing Superman, he speaks his experience during Superman: The Animated Series (1996) when Brainiac took over his mind to exploit Wayne Enterprises' resources in Knight Time (1998). Seeing as how Batman put his own painful experience behind him and moved on, he expected Superman to do so as well.