When Superman and Flash are walking out of the room in the last couple minutes, they walk towards what, given how perspective works, should be a 2 inch tall flag. However, when Superman arrives at it, it's just as tall as he is.
Hawkgirl's wings are what enable her to fly, so does that mean Lorder Hawkgirl, after being shot by the power disruptor, can still fly or have her wings just become useless?
When the League needs entrance to the medical room at Arkham, Joker asks for a password. Martian Manhunter reads his mind and telepathically tells Superman the password. Supes says it aloud but the Joker states that Wonder Woman was supposed to say it. Why could Martian Manhunter not pick that up when he was reading the Joker's mind?
Where does the alternate-Batman swing down from at Arkham? Judging from the direction he comes from and where the line seems to be positioned, he seems to be swinging in from a point above and in front of the main building and several stories higher...but in the opening shots we see there's nothing there.
How does Lex know which J'onn to blast? They've both shape-shifted into roughly the same form, and the J'onn that circles around after Lex blasts GL doesn't look that hostile toward Lex. Yes, they look different but how does Lex know the evil J'onn has particular differences? (Lex might not care too much, but his pardon does hinge on being sure not to hurt the good guys.)
So...what happened to the Justice Lords at the end? Did they get their powers back eventually? And what did the Justice League do with them? Imprison them on their Earth, or send them back to the alternate Earth? And if the Lords are back on their own world, what's to stop them from using the portal to just go back and start the whole thing again? (Alternate-Batman might stand on principle and destroy the portal after his comrades are sent back, but alternate-J'onn could telepathically get the information from him to recreate it.)
Batman had a lot on his mind, but it seems odd that he didn't make sure that alternate-Batman was securely locked up, or anticipate that his alternate could escape so easily.
Does Lex really have much chance as a pardoned super-villain of successfully going into politics, much less becoming President? In the comics it works a little better because the general public doesn't know he's a villainous mastermind but in this animated series he's fought the League publicly on numerous occasions, formed the Injustice Gang, etc.
When alternate J'onn loses his shapeshifting powers, shouldn't he revert to his natural Martian form as seen in "Secret Origins" and "Tabula Rasa" rather than his Justice Lord form?
Why did the head of the Superman robot say "Thanks" when it was knocked off by Wonder Woman?
When Superman breaks out of his cell, he is wearing a metal band around his eyes (presumably to prevent him from using his heat vision), but this band is missing on the viewscreens that Justice Lord Batman was viewing before the breakout.
Superman Robot: You must be stopped.
Green Lantern: A robot?
Superman: I built mine to take over for me when I had to be away.
(more robots walk in)
Green Lantern: Looks like the other guy had the same idea... in spades!
Batman: They'd love it here, don't you think?
Alternate Batman: Who?
Batman: Mom and Dad, they'd be so proud of you.
Alternate Batman: Just drive.
Batman: You grabbed power.
Alternate Batman: And with that power, we created a world where no 8-year-old boy will ever lose his parents... because of some punk with a gun.
Batman: You win.
Superman: Wait here - you're dead, remember?
Flash: Hey, the costumes'll tip them off anyway...
Wonder Woman: We'll just say it's a fashion choice.
Batman: You've thought of everything.
Alternate Batman: No - just everything you'll ever think of.
Flash: So you're not such a Boy Scout after all.
Superman: Never even made it to my first merit badge.
Flash: Hey, (my alternate) was the conscience of your group, and that means I must be...
Green Lantern: C'mon, Jiminy.
Batman: How else can we stop them?
Superman: You're the smart one - you figure it out.
Batman: I think he likes you.
Flash: Must be my magnetic personality.
Flash: You figured a way out of here?
Flash: Don't you mean 'not yet'?
Batman: No, I mean not going to.
On Toonami in the UK, this is the finale of season two.
At least three Batman villains, the Riddler, Two-Face and the Ventriloquist (with his dummy - note the lobotomy holes) are also present in nonspeaking roles. The one with the mustache may be Deadshot, although he has never been identified without a mask in any animated series.
Diane Pershing and Mark Hamill reprise their Batman: The Animated Series roles of Poison Ivy and the Joker.
Superman righting the flag
Referencing Christopher Reeve's character doing the same thing at the end of the second Superman movie.
During the Batman vs. Batman scene in the Batcave, the Nightwing, Batgirl, and Robin costumes are all hung up, just like they were in Batman Beyond. In the other DC animated series (editor's note: which may not necessarily be part of the Justice League setting) Nightwing is a solo fighter, Batgirl is Batman's Gotham City partner, and Robin is the leader of the Teen Titans. So in the Justice Lords reality, this could mean one of two things; The Three could be back to working for Batman, or Batman could have forced the three into early retirement as a form of protection.
Green Lantern: Come on, Jiminy!
The Green Lantern calls the Flash 'Jiminy' because he said he must be the conscience of the League. GL was referring to Jiminy Cricket, a cartoon character who originally appeared in the1940 Disney's adaptation of Carlo Collodi's Pinocchio. He acted as Pinocchio's self-appointed conscience and a comic foil who accompanied him on his adventures -- just like the Flash.
Batman: 91939 - It's the numbers I use.
Batman's code numbers appear to be an in-joke reference to the date September 1939 (i.e., 9 - 1939, or 9/1939). That would be the cover date of Detective Comics #28 - the issue where Batman's origin appeared.
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