Dark Reprise: The JLU theme song gets one when the Brainiac copies transform into the Justice Lords.
Deus Exit Machina: the JLU are stranded on the Watchtower, leaving it up to the seven founders to deal with Brainithor by themselves.
The Fellowship Has Ended: the founding members decide to disband the Justice League at the end of the episode. Green Arrow convinces them to change their minds, to which an impressed Batman has a Call Back to why he recruited Green Arrow in the first episode.
Generic Doomsday Villain: Lex Luthor figuratively gets under Brainiac's skin after the latter literally got under his skin by accusing him of being one of these. Luthor points out that Brainiac had no real plans of doing anything with its vast store of knowledge and that it had no real reason for destroying the universe. Brainiac realizes Luthor has a point and agrees to a Fusion Dance so they can actually do something with all of that power and knowledge.
Heroic RROD: The Flash ends up disappearing into the Speed Force after defeating the fusion of Lex Luthor and Brainiac, but the trope is ultimately subverted when the rest of the Justice League is able to locate the portal and pull him out of the Speed Force.
Mythology Gag: Flash's Justice Lord counterpart is made to look like Zoom.
Neck Lift: A very angry Superman does this Luthor when he thought Flash died.
Oh, Crap: The League when Flash disappears. Even Batman is stunned.
Luthor himself when he saw that part of his armor is destroyed when the Flash punches him, and realizes the Flash is racing around the world to punch him several times, with increasing intensity.
Lord!Flash: Slacker! Child! Clown! We have no place here among the world's greatest heroes! Flash: Says you! I got a seat at the big conference table. I'm gonna paint my logo on it! (pow)
Take My Hand: As she reaches into the Speed Force that the Flash had disappeared into, she tells him to take her hand as she and the other five remaining founding members try to pull him out. As they're pulling him out, you might notice that Shayera is holding him by the wrist and that he didn't actually take her hand.
Tempting Fate: Flash makes quick work of his double by vibrating his hands and running the double through with it. He makes the following remark, yet he has to do it again to defeat Brainithor.