Lex Luthor's betrayal of the light, if only for how casually he managed to throw the team and the light for a loop.
The attack on the watchtower. For the first time in a while, the mooks aren't easy for the league to take down, and it is a glorious battle for survival.
For that matter, they managed to give Dr. Fate and Hal Jordan, two characters with a big Story Breaker Power a hard time.
Ms. Martian, Wonder Girl, Superboy and Wolf make a desperate escape from Smalville from another army of parademons and suicide jockeys.
On the villains side, Kara's brutal beatdown of Superboy. Though he might fight like a kryptonian, Kara really didn't give him much room.
The fight for the future. 5 years into the future, the remnants of a new Team escort Bart Allen to his time machine to return to the past and prevent Darkseid from destroying everything. Facing Parademons, a being with kryptonian and maritan dna and evil wally, they fought to the last man, and even in death, the last 2 members faced it with honor.
The Car Chase and battle between Nightwing, Starfire and Red Hood's boys.
The battle in DC. Risking everything to save the future, the team exposes Godfrey as the fraud he is, stops the league's suicide attack, and a battle with the furies and their armies begins. The Justice League even gets in on the action, making this the first full scale brawl that needed the league and team since the reach endgame challenge.
Aquaman vs King Shark. The 2 kings locked in battle with the fate of a kingdom resting in their fight.
Black Manta's Villainous Rescue and the subsequent Enemy Mine was also rather cool if only because of how well they worked together to drive Nanue off.
For that matter, Manta's Kansas City Shuffle to escape prison during the battle. "Nobody leads Black Manta's army but Black Manta."
One has to give props to the author for creating a story that not only provides a more satisfying conclusion to the series than we got, but also managed to weave his storylines together in such a way that it feels just like the show proper in execution, mystery and intrigue.