Part 1: The Crisis begins and Earth-38 is under the gun from the Anti-Matter wave. Harbinger brings Green Arrow, The Flash, Batwoman, Sara Lance, and Ray Palmer to Supergirl's Earth to make a stand. Along the way, Harbinger also brings Superman and Lois from Argo City right before it's consumed by the Anti-Matter wave. The team fights for as long as they can to let as many people escape Earth-38 as possible. Millions are saved but, unfortunately, Oliver Queen dies as everyone is transported to Earth-1.
Part 2: Clark, Lois, and Iris begin Earth-hopping to find which Superman fits their Paragon role, and Kate and Kara do the same but for Bruce Wayne. Barry, Sara, and Mia discover a Lazarus Pit with the hope that they can revive Oliver, which ends up not working. The hunt for Superman ends when they find Kingdom Come Superman (played by Brandon Routh), who is momentarily controlled by a Book of Destiny-wielding Lex Luthor. Kara and Kate learn the Bruce Wayne they found is a broken man, having killed most of his famous enemies and his Earth's Superman, so the two return after taking the man out. Kate learns that she is, in fact, one of the Paragons along with Barry, Sara, Kingdom Come Clark and Martian Manhunter.
Part 3: Flash, Cisco, and Pariah break into the Anti-Monitor's lair and discover the Flash from Earth-90 has been powering his anti-matter machine. The group also meets Black Lightning, who helps them slow down the wave before Earth-90 Flash sacrifices himself. Diggle, Constantine, and Mia are still trying to resurrect Ollie and ask for Lucifer's help before being sent to Oliver's version of the afterlife. They meet him but don't get much time before the Spectre shows up and whisks him away for a new mission. After Ray, Ralph, and Iris track down Ryan Choi – the last paragon – everyone converges on the Waverider and learns that the Anti-Monitor had that planned all along. He reignites the anti-matter wave and takes everyone out for good... except the seven paragons.
They find themselves at the Vanishing Point – a place outside of time – and they're the only remaining people in existence. Before they can truly get to figuring out what to do, Kingdom Come Superman disappears and is replaced by Lex Luthor. When he had the Book of Destiny in Part II, he had rewritten himself as the Paragon of Truth in a bid to save himself. Now, they're one Paragon down and have no plan for stopping the Crisis.