Anticlimax Boss: The team doesn't even get to fight Vandal Savage before his death.
Badass Decay: Oh Light, what happened to you? Aside from a few mentions in the first couple chapters, and some influence in the middle, the Light on the whole is doing a whole lot less in this fic, especially after Lex Luthor betrayed their operations to the League.
On another note: Mammoth. Although he was among the strongest of the mooks, he gets taken down by Static's electricity on his own.
In a Bad Future, Darkseid successfully took over Earth, destroying most of the cities and killing almost all the heroes. Humans were forced to do backbreaking labor while worshiping him as he tortured them. If any of his minions ever failed him once, he would give them 50 lashes. Fail him a second time, and he would have them banished to a place so horrifying that no one would speak of it, a place where he banished his son Kallibak. It's also revealed that when Comic Book/Vandal Savage managed to kill a bunch of superheroes for him, Darkseid vaporized him because he wanted the heroes brought to him alive so he could torture them first.
The attack on the Watchtower definitely got reader's blood pumping.
"Episode 11: Past and Future Revelations" spends its time split between the present and future, but it ends with a Final Battle, 2 deaths, and the end of Darkseid's first attack on earth.
Jerkass Woobie: Kara is definitely no saint in this series, even starting off evil. However, she gets more sympathetic the longer the story goes, as her quest to redeem herself slowly makes her more sympathetic as she goes.
Like You Would Really Do It: In Chapter 55, Superman dies. Oh yes, because everyone knows that superheroes stay dead when they're killed, especially one as big as him.
Magnificent Bastard: Lex Luthor and Vandal Savage are in full out magnificent mode. Redirecting the Team from important places, planning attacks months in advance, and in Lex's case, planning the downfall of the Light in order to gain more power for himself.
Moral Event Horizon: While no nice person by any stretch, when Granny Goodness orders her own Furies killed when they refuse to return with her to be her fall people, she crossed this line.
Villain Sue: Invoked with Klarion, as he continues to be curb stomper all the way up until his defeat. On the other hand, despite being practically unbeatable one on one, his weakness via familiar gets brought up again, allowing the League and Team to FINALLY defeat him once and for all.
They Wasted a Perfectly Good Character: Despite being the only Runaway to join The Team, Static doesn't actually get to do a lot once he joins, mostly acting in a supporting role than doing anything really significant.
The Woobie: M'gann. She still carries a lot of guilt for her actions back in season 2 with her, and doesn't really get over it until she marries Conner