The long-awaited rebirth of the greatest superhero team of all time: Batman, Superman, The Flash, Wonder Woman, Hawkgirl, Green Lantern and Martian Manhunter.
After Lex Luthor escapes from prison, Gorilla Grodd baits him into joining the new Secret Society with a piece of Brainiac technology. Luthor, the Key, and Doctor Polaris steal the Spear of Longinus from Blackhawk Island despite the efforts of Flash, Fire whom Flash had a crush on at the time, Shayera, and the last surviving Blackhawk to stop them.
Shayera agrees to meet with Carter Hall, an archaeologist who has discovered Thanagarian artifacts from ancient Egypt. With a suspicious Batman eavesdropping, Carter reveals himself to be her reincarnated lover from the past and Hawkman to a confused Shayera. The Shadow Thief attempts to steal the artifacts, which results in the destruction of the tomb, and leaves the question unresolved.
Supergirl, Stargirl, S.T.R.I.P.E., and Green Lantern help Warlord liberate Skartaris (a hidden world inside the Earth's core) from Deimos, a brutal dictator while protecting a very large piece of Kryptonite from Metallo and Silver Banshee.
Wonder Woman protects the body of the Viking Prince from Legion agents who want it for reverse engineering of invulnerability powers. Troubled by his isolation, J'onn leaves the Justice League to better understand humanity.
Orion attempts to understand Flash's antics as Wally and Batman battle four of Flash's rogues that attack the museum that is opening in his honor. Even though the new museum was all but wrecked, the occasion still turned out to be a "good day," according to Flash.
Deadman convinces Superman, Batman, and Wonder Woman to help him retrieve the stolen souls of a mystic order of monks that the Secret Society has stolen. They force the Secret Society to retreat from Gorilla City, ending Grodd's attempt to turn all people on Earth into apes. Back at a general meeting in the Secret Society's HQ, Lex Luthor cites that Grodd's plan failed and his "master plan" (turning everyone on Earth into apes) was silly, and shoots him, taking over leadership of the Secret Society.
General Wade Eiling from Cadmus steals the "Captain Nazi" super-soldier serum and injects it into himself to "protect" the world from metahumans. With the more powerful League members busy, Green Arrow leads Stargirl, S.T.R.I.P.E., Shining Knight, Crimson Avenger, Vigilante, and Speedy against him. Eiling only stops short of killing Shining Knight when a civilian points out that Eiling's reason for attacking the heroes is non-existent, as his entire reason for the attack was to rid the world of meta-humans and he was the only one there with super powers.
Magic and science collide, placing Lex Luthor and Flash's minds in each other's body. The Justice League must now contain a super-speed powered Luthor on the Watchtower while Flash tries to hide the reversal from the Secret Society.
Roulette restarts Metabrawl, this time with an all-female fight card ("Glamour Slam") made up of mind-controlled Justice Leaguers. First, the Huntress and Black Canary are set against Vixen and Hawkgirl, and then the four must contend against Wonder Woman.
Supergirl, Green Lantern and Green Arrow are kidnapped and taken to the 31st Century by Brainiac 5 and Bouncing Boy of the Legion of Super-Heroes, where Supergirl is destined to embark on her very last mission – a battle against the Fatal Five and the Legion itself.
The Hawkman story concludes here when Shadow Thief captures Green Lantern, Shayera and Hawkman, then forces them to watch a vision of their past selves developing an ancient society of Egypt with Thanagarian technology. It turns out Shadow Thief is a villain from Carter Hall's mind that was released when he touched the Absorbacron in "Shadow of the Hawk." Hawkman defeats Shadow Thief and leaves. John Stewart, not wanting to have destiny play out his life, does not get back with Shayera, even though the two say they love each other. GL goes back to Vixen, but not before he tells Shayera about Rex Stewart (Warhawk), their alleged future son. In the final scene of the episode, Shayera asks Batman about this future son, but the credits roll before he can answer.
Luthor and the Secret Society refit their headquarters and fly into deep space in a last-ditch attempt to reanimate Brainiac. En route, Tala frees Grodd, who leads a mutiny of other disaffected villains against Luthor and his supporters. Luthor uses his intellect and resourcefulness to counter his various adversaries' powers; Grodd's mind-control ability is used against him, forcing him to step into an airlock, from which he is released into the void. Luthor uses Tala's magic in an attempt to reconstitute Brainiac, but instead resurrects Darkseid (with Brainiac enhancements), who makes clear his plans to lay waste to Earth before destroying the Secret Society's headquarters. Darkseid returns to Apokolips just in time to stop a war between the two factions of his Elite fighting for power, and reveals to them his plans of massive invasion. Luthor and the surviving Secret Society members turn to the Justice League for help.
The Justice League reluctantly teams up with the remnants of the Secret Society to repel Darkseid's full-scale invasion of Earth. As the League and Secret Society members battle the Apokolips fleet across the planet, Superman, Batman, and Lex Luthor take on Darkseid atop the Daily Planet building.