As alien invaders who were accidentally awakened on Mars begin to take over the Earth, Superman and Batman rescue Martian Manhunter, who telepathically summons Wonder Woman, Hawkgirl, The Flash, and Green Lantern to help stop the invasion. Superman gathers everyone at the newly built Watchtower, funded by Batman, and asks them to be part of a team, which he dubs the Justice League.

Green Lantern surrenders himself to robotic Manhunters to stand trial for the destruction of a planet. While Flash acts as Green Lantern's attorney, the rest of the League discovers that Kanjar Ro helped the Manhunters frame Green Lantern.

A nuclear submarine is attacked in the Atlantic, forcing the League to come face-to-face with Aquaman and his Atlantean army. Aquaman follows Superman's advice to go to Metropolis and take his problems up with the various governments of the world. When a mercenary, Deadshot, attacks Aquaman, the League steps in. Aquaman discovers that Lord Orm, his own brother, was behind the attack. Orm takes Aquaman and his infant son and places them on a cliff over a vein of molten lava, leaving them to die. To save his son, Aquaman sacrifices his own hand.

Having spent nearly eight months with the League and feeling she owes her mother Hippolyta an explanation for her leaving Themyscira abruptly to fight in the Imperium invasion, Wonder Woman returns to her home only to encounter Sorcerer Felix Faust who threatens to keep her home population transformed into stone if she does not gather artifacts for him. He uses the artifacts to release Hades from Tartarus. The League succeeds in exiling Hades and his minions, but Wonder Woman is exiled from Themyscira for allowing the men of the Justice League to help.

Superman and Martian Manhunter are abducted by extraterrestrial slave traders and sold to the planet War World, whose despotic ruler Mongul pits aliens against each other in mortal combat in an enormous colosseum. Hawkgirl and Green Lantern set out to rescue them.

The Flash and Green Lantern uncover a plot by Gorilla Grodd to destroy Gorilla City, a hidden city of hyperintelligent talking gorillas in Africa. Grodd has a device that allows him to control the minds of others and uses stolen gorilla technology to conquer all of Central City and put its inhabitants under his control. Locked inside the force field-shielded city, Flash and Green Lantern work together with Solovar, Gorilla City's chief of security, to destroy the enemy from within before Grodd carries out his revenge.

Absent: Superman

Flash, Green Lantern, Martian Manhunter, and Hawkgirl are accidentally transported to a parallel world and discover the Justice Guild of America, who are comic book characters in the Justice League's world. As they traverse this world and help the Justice Guild of America fight the Injustice Guild, they soon discover that not everything is what it seems since the end of their comic series.

Note: The episode is dedicated to Gardner Fox, a Golden and Silver Age comic writer who co-created both the Justice Society of America (JSA) and the Justice League of America (JLA), the comics on which the Guild --and this series, respectively -- are based.^[4] Originally, the showrunners wanted to use the JSA, but DC Comics publisher Paul Levitz felt that the story was inappropriate, so they altered the names and designs of the team.

Jason Blood and his alter-ego Etrigan the Demon seek the assistance of the Justice League in preventing the Philosopher's stone from falling into the hands of his ancient enemy, the sorceress Morgaine le Fey.

Green Lantern's old friend Rex Mason, now working for a shady industrialist, suffers an "accident" arranged by his jealous employer Simon Stagg and is transformed into the superhero Metamorpho.

The Justice League returns from a mission in space to find the world transformed; a result of villain Vandal Savage feeding information to his past self in the 1940s, allowing him to help the Nazis win World War II. The League travels back in time themselves to stop him, and fight Nazis alongside WWII-era heroes Easy Company, the Blackhawks, and Steve Trevor.

The League is tricked into defending Darkseid's homeworld of Apokolips against the threat of Brainiac, despite Superman's skepticism and his anger at what had last occurred between him and the ruler of Apokolips. The team solicits the aid of the New Gods, including Orion, Lightray, and Highfather. The resulting destruction of Brainiac's base is thought to be the end of Darkseid, although Superman believes otherwise.

Small time crook John Dee volunteers for an experimental treatment while in prison. While the authorities are distracted by a mass prison break led by Volcana, Luminus, Copperhead, Solomon Grundy and Firefly, John Dee overdoses on the treatment and becomes the dream-controlling Doctor Destiny. Destiny takes telepathic control of most of the League in their sleep and puts them in nightmares where Flash can't stop running, nobody knows Green Lantern due to his status as a member of the Justice League, Superman being unable to control his powers which led to the deaths of the people he knows, and Hawkgirl is buried alive. The League members become trapped in their dreams and unable to wake up. This leaves only Batman and Martian Manhunter left. Martian Manhunter tries to force them awake, while Batman, resisting sleep goes to confront Doctor Destiny.

Wonder Woman befriends the princess of Kasnia, a jet-setting party girl who is reluctant to end her wild ways to get married. Unfortunately, her fiancé is the immortal Vandal Savage, and he already has plans for both the throne and the Justice League. Wonder Woman and Batman must stop Savage, while Flash, Green Lantern, and Martian Manhunter take out Savage's new Rail Gun satellite.

Note: This is the first episode of the Justice League series in which Batman appears as Bruce Wayne.

Kilowog crashes to Earth, seeking Green Lantern's help to rescue other members of the Green Lantern Corps from the psychic, would-be conqueror Despero. He also explains that Green Lantern's former mentor and lover, Katma Tui, is one of the captives. After facing Despero and losing, Green Lantern has to retrain himself to use his power ring to help the League end Despero's reign. Flash, Hawkgirl and Martian Manhunter accompany Kilowog to Despero's planet to help Green Lantern stop him.

In an alternate reality, the Justice League launches an assault on the White House, where Superman kills President Luthor in retaliation for the Flash's execution by Luthor. Two years later, the League, now called the Justice Lords, rule the planet with an iron fist. Justice Lord Batman discovers the dimension where the Justice League lives. The Lords cross over and trap the League in a force field. They then take the League's places, attempting to make this Earth like their own. After finding their way back to their world, the Justice League ends up having to turn to their world's version of Lex Luthor for help.

An ancient lunar crystal called the Black Heart is discovered. Unbeknownst to the members of the Justice League, it harbors an evil snake spirit with the ability to possess its bearer, and hum or whistle an eerie evil tune. The crystal's power contaminates almost all of the League, except for the Flash, who must save the League from a weapon that will destroy both the Sun and the Earth.

Doctor Fate and Aquaman rescue Solomon Grundy, intent on using him to help battle an ancient evil. Superman, Hawkgirl and Wonder Woman are conflicted about this goal.

Note: The pairing of these heroes is an homage to the Marvel Comics superhero team The Defenders. The plot is based upon H. P. Lovecraft's Cthulhu Mythos.^[6]

A band of supervillains (composed of Metallo, Kalibak, Livewire, Weather Wizard, and Toyman) team up to get revenge on Superman. When they attack Metropolis, Toyman shoots an experimental weapon at Batman and an injured Wonder Woman, but Superman sacrifices himself to save them and is seemingly vaporized. The League attempts to cope with the loss of Superman by defending Metropolis in his absence, save for Batman, who does not believe Superman is truly dead and begins investigating on what actually happened. Eventually, Lobo arrives at the Watchtower and nominates himself as Superman's replacement, but he does more harm than good. Superman wakes up 30,000 years in Earth's future, but the sun has turned red, removing his superpowers. He encounters a humbled Vandal Savage, the only human left alive after an attempt at world domination staged a few months after Superman's disappearance. Savage reveals he had been working on a time machine, but he is immortal, and he cannot exist at the same time as his previous self as it would cause a paradox. Superman can go back to a time where he doesn't exist, i.e., after his 'death'. With knowledge of past Savage's crime, he goes back in time, reunites with the League and informs them of Savage's plot. Lobo is sent on his way. In the future, the desolate wasteland is replaced with people and a city as a thankful Savage disappears from existence.

With his Gwynplaine Entertainment Company (a reference to The Man Who Laughs) the Joker takes over TV stations in Las Vegas, announcing that he has placed a series of bombs that will destroy the Strip in 22 minutes and 51 seconds if they are not stopped by the Justice League. With the whole world watching, the League must first get past the Joker's own super-team, the Royal Flush Gang. However, the threat imposed by the Joker is not as simple as it seems, and Batman must track down his location to stop him.

Note: This episode is notable as a 'hidden crossover' with Teen Titans, as the Royal Flush Gang is voiced by the five principal actors from that series. The gang's designs are also based on the Teen Titans voice actors.^[7]

After saving two worlds, the members of the Justice League decide to take a break to celebrate the holidays. The Flash spends his Christmas Eve with the children of an orphanage, who ask that he find them a special animated toy duck. The popular toy is broken by the Ultra-Humanite, who eventually comes around and helps The Flash. Green Lantern and Hawkgirl show each other how they spend the holidays. Green Lantern engages in a snowball fight with Hawkgirl. Hawkgirl responds by starting an interplanetary barroom brawl. Batman spends Christmas on Watchtower duty. Meanwhile, Superman invites Martian Manhunter over to Smallville for Christmas Eve with his adoptive parents. Although Martian Manhunter is initially uncomfortable, he eventually learns to enjoy Christmas and inadvertently gives the Kents a gift in the form of a heartfelt Martian song.

Note: This was the first and only standalone episode of the series.

After Earth is attacked by a Gordanian battleship, the League is aided by an army of Hawkmen from Hawkgirl's home planet of Thanagar. The Thanagarians offer to help Earth build a shield to defend against the Gordanians, but Batman discovers that this is just a ruse. Hawkgirl finds herself torn between her allegiance to Thanagar and her commitment to the Justice League, as well as between her betrothal to the Thanagarian commander Hro Talak and her budding romantic love for Green Lantern.

When the Watchtower has a sudden power drain, the Justice League recruits Static to jump start their station before it reenters the atmosphere. Unbeknownst to either Static or Gear, the power drain also releases Brainiac from his confinement. Static and Gear manage to bring Brainiac down, but the villain has a loophole left to slip through.

Static faces off against his idol Green Lantern (actually Sinestro in disguise) when he causes chaos all over town.