Batman and Wonder Woman arrive at the Fortress of Solitude to celebrate Superman's birthday. They soon discover that he is being held captive by Mongul in the fortress, and is under the effects of a wish-fulfilling parasitic plant known as the Black Mercy, which has left him prisoner in a dream where Krypton was never destroyed and he leads an idyllic life. Batman and Wonder Woman find themselves forced to snap him out of this fantasy, knowing it could prove disastrous for the League.

Wonder Woman teams up with two super-powered brothers, Hawk and Dove, after learning that Ares plans to escalate a civil war raging in Europe. The pair soon find themselves assisting her when they learn that Ares' scheme involves giving one side access to a powerful war machine called the Annihilator which he asked Hephaestus to forge for him.

Green Arrow and Question investigate Supergirl's disturbing dreams, after she begins experiencing them more recently. Their investigation soon leads them to discovering a secret organization called Cadmus, who have created a clone of Supergirl named Galatea whilst she had been recovering from her fight against Superman on Earth. All three soon become involved in investigating what Cadmus is planning, unaware of who was involved in Galatea's creation.

Mordred rebels against Morgaine le Fey and uses the Amulet of First Magic to remove all adults from Earth and lord over every child on the planet. Seeking to stop this, le Fey discovers a loophole that can allow the Justice League to stop this, and transforms Superman, Batman, Wonder Woman, and Green Lantern into children to combat Mordred. Despite some setbacks, the group swiftly do what they can to thwart Mordred's plans being conducted from an amusement park.

While on a stakeout in Gotham City to stop some members of Intergang, Wonder Woman and Batman encounter the centuries-old enchantress Circe who transforms the former into a pig as revenge against Diana's mother Queen Hippolyta. Batman and Zatanna work together to return her to normal, while B'wana Beast attempts to find the "Wonder Pig" before she's butchered at a slaughterhouse.

Batman, Green Lantern, and Wonder Woman find themselves in Gotham City in the future, aided by the surviving members of the Justice League (Rex Stewart / Warhawk, a middle-aged Static, Batman and the elderly Bruce Wayne) of that period in defending against a powerful group of Jokerz. The time travelers soon learn that Chronos is making irreparable damage to history that could erase the universe. Aided by their future allies, the group thwart Chronos' plans, although their visit leaves Green Lantern with some difficult news concerning his future.

With most of the League unavailable due to different emergencies, the League's founding members battle a fusion between Luthor and Brainiac. Lex and Brainiac temporarily escape, using material from the Dark Heart stored by Cadmus to merge their bodies permanently. The League is tasked with battling robotic Justice Lords, and the Flash saves the day when he runs around the world numerous times in order to separate and defeat the Luthor/Brainiac fusion. However, he runs so fast that he almost dies as his body is transported to the Speed Force. The League holds a conference noting that they are disbanding the League due to recent events. However, Green Arrow tell them they have saved the world too many times to give up when times are tough. Superman agrees to keep the League, but he promises that there will be changes.

Fifteen years into the future of Batman Beyond, Terry McGinnis learns that he is Bruce Wayne's biological son, and confronts Amanda Waller, who reveals that she created Project Batman Beyond to continue Wayne's legacy. She knew the world would always need a Batman, so she conspired to first overwrite Terry's father's DNA with Bruce's, and then, at the right age, send an assassin (Phantasm) to kill Terry's parents. However, Phantasm did not go through with it, telling Waller it would violate Batman's strong moral code. Terry's father was later killed by Mr. Fixx anyway under Derek Powers' orders. She explains that he is not Bruce's clone, but his son, and that he can always choose to live life on his terms and not have to be like Bruce, who pushed his loved ones away out of devotion to his crusade. She shares that while he may not have Bruce's intellect, he does have his heart. Encouraged, Terry plans to propose to Dana and goes home to take care of an elderly Bruce before flying off into the night as Batman to assist Superman with a case.

• According to Stephen Harber, the episode was originally intended to be the series finale for Justice League Unlimited and the DCAU in general.^[10] The decision to end on a Batman-heavy episode was planned as a way of bringing the series full circle, ending the same way that the premiere Batman: The Animated Series episode ("On Leather Wings") began with police spotting a bat-like figure in the night sky.

After Lex Luthor escapes from prison, Gorilla Grodd baits him into joining the new Secret Society with a piece of Brainiac technology as Luthor can hear Brainiac in him. Luthor, Key, and Doctor Polaris steal the Spear of Longinus from Blackhawk Island despite the attempts of Flash, Fire, Hawkgirl, and the last surviving Blackhawk to stop them.

Orion attempts to understand Flash's antics as Wally and Batman battle four of Flash's Rogues like Captain Boomerang, Captain Cold, Mirror Master, and Trickster who attack the opening of the Flash Museum.

General Eiling steals the Captain Nazi super-soldier serum and injects it into himself to "protect" the world from the Justice League. With all the League members with actual powers busy, Green Arrow leads Stargirl, S.T.R.I.P.E., Shining Knight, Crimson Avenger, Vigilante, and Speedy against him when he attacks a parade they were hosting. Eiling only stops short of killing Shining Knight when a civilian points out the hypocrisy of Eiling's actions: his goal was to rid the world of metahumans, but he had been using superpowers against heroes without powers who disagreed with him.

Trying to learn more about the Secret Society, magic and science accidentally collide swapping the minds of Lex Luthor and Flash. The Justice League attempts to contain a super-speed powered Luthor on the Watchtower, while Flash tries to hide the change from the Secret Society. Lex learns of Flash's identity, but it is of no use to him. Flash also allows the League to learn about Lex's new plan for the society and learn about the scale of their operations.

Needing money for the Secret Society to search for Brainiac, Lex tasks Roulette with restarting Metabrawl, this time with an all-female fight card called "Glamour-Slam", made up of mind-controlled Justice League members. First, Huntress and Black Canary are set against Vixen and Hawkgirl, and then the four must contend against Wonder Woman. They ultimately are able to break out of their mind control through inflicting pain on each other and scare away the audience and capture Roulette and Sonar. However, they do not learn anything about who she works for.