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Giving Brandon's Superman gray hair at the temples isn't just a Kingdom Come reference, it's a crucial piece of DC history, as well. In the original Crisis on Infinite Earths story, the Superman of Earth-2 was a central character. While Earth-2 is now long gone in the Arrowverse, it served a very different purpose in the classic DC Comics, where it was the home of the original versions of their heroes and villains as they were first published. So the Superman of Earth-2 was the one who first appeared in Action Comics #1, he eventually married Lois Lane, became editor-in-chief of the Daily Planet (as Clark is here), etc. His hair was gray at the temples and his "S" was slightly more stylized to make it easier to distinguish him from his younger Earth-1 counterpart. Brandon's Superman seems to be filling that role here
Kevin Conroy discussed with Entertainment Weekly how the "Crisis" role took him by surprise, stating how the experience of playing Batman for the first time in live-action "threw him" at first. "I never approached this character from that physicalized aspect. I always just inhabited him with my voice," Conroy said. "When you do that in a recording studio, it's a very intimate experience and you're sort of living in your own imagination. You do it with your eyes closed and you're in this other world, and you have Mark Hamill feeding you [need], and the other actors (because we always recorded together in the booths.)" "To actually be on the set, in the physical world, and to be walking as the character and inhabiting the character in three dimensions, it was a real transition for me," he added. "It did take a while to get used to, I have to admit. I was surprised because I know the character so well."
Executive producer Marc Guggenheim spoke of Kevin Conroy, "He is stupendous, He is Bruce Wayne. [It's] just a lot of fun to see this actor who we all mainly know from voice work being on camera. It was really exciting." Conroy's appearance in "Crisis" is the result of a dream. "One of the things that was always on my bucket list is that I wanted to see old Bruce Wayne," says Guggenheim. "We talked about a variety of different casting possibilities, but [Legends of Tomorrow showrunner] Keto Shimizu, who is a huge animated Batman fan, pointed out that Kevin is the right age. We reached out to Kevin and he couldn't have been more lovely and more game for it."
Sara tells Harbinger that she promised her crew no more crossovers, a breaking the fourth wall joke referring to how the Legends weren't part of the Elseworlds crossover.
Earth-99 is a reference to when Batman Beyond came out in 1999. Kevin Conroy played an older Bruce Wayne (actually much older than this one), who took a new young man under his wing to make sure that there would always be the new Batman of the future.
The Earth-99 Bruce Wayne has mementos/trophies of a bloody Joker card, The Riddler's cane, Mr. Freeze's jar that contained the ice sculpture of his wife Nora Fries, and possibly a plant under glass that may signify Poison Ivy and the glasses of that Earth's Clark Kent.