"Secret Origins" is the series premiere of Justice League. It originally aired as a full-length movie, on November 17, 2001. Subsequent re-runs divided the episode into three parts.
Two astronauts explore the terrain of Mars. One stumbles onto the entrance to an underground cavern, at the end of which is a massive, ornate door. He wedges his pickaxe into the door's lock, and forces it open. The doors open, and something massive rushes out, reaching for him...
Two years later: Batman makes a brief trip to the outskirts of Metropolis, spying on a satellite communications facility operated by Wayne Tech. As he watches, three employees of the facility exchange amiable good-byes with their co-workers, but as soon as they are alone, begin conversing in an alien language and tampering with the equipment. Batman appears and attempts to subdue them, but each of them fight back with amazing speed and strength. Batman corners one on top of the roof dish, but it turns the tables on him. Then Superman arrives and sends it running. Before they can deal with them, Superman sees strange images in mind and is rendered unconscious. Batman grabs him as the three mysterious scientists detonate the satellite. As Batman sees the three scientists, they twist their bodies into positions that are inhuman, but they flee into the forest.
The two heroes share a reserved greeting; two years after Darkseid's brainwashing, Superman has regained the majority of the world's trust, but wonders if Batman is still in the minority. Batman explains that this station is the latest in a series that has been sending strange encrypted signals into space. Superman offers his help, but Batman declines. Superman hands him a communicator to use in case he needs help; Batman is skeptical, but places it in his utility belt and keeps it anyway.
In the nation's capital, J. Allen Carter, one of the two astronauts from the Mars expedition and now a U.S. Senator, proposes a bold plan for total nuclear disarmament. He champions Superman as Earth's protector, believing that the Man of Steel is both reliable and more than capable of handing any threat to the Earth. Superman embraces the idea, despite protests from the military and other sources. These even include other heroes, such as Central City's The Flash, who remarks: "I'm the fastest man alive, and even I can't be in five places at once".
As Superman works to disarm the world's nuclear weapons, Batman continues his investigation. He traces the three fake scientists to a warehouse in Metropolis, where he discovers the three real scientists, unconscious, inside alien-looking containers. Then a guard dog appears, which turns out to be an alien creature, and attacks. Batman is outmatched, and calls for help.
Superman arrives, and manages to save Batman, but then both of them watch as a meteor comes down from the sky and crashes into the heart of Metropolis. From the crater, a massive alien vehicle appears, and without preamble makes its hostility clear: it begins attacking the police and fire units nearby. More meteors crash, giving rise to more vehicles. Superman and Batman throw everything they have at the creatures, but seemingly to no avail. While preparing to fight again, Superman suffers another psychic migraine; entranced, he flies away.
The world goes into a panic about the new alien invasion, and the apparent absence of Superman. On Themyscira, Princess Diana notices signs of trouble in the outside world, but her mother, Queen Hippolyta, tells her that it is none of their concern, as the Gods protect Themyscira.
Batman flies after Superman, tracking him to a U.S. Army base. Inside, they find a green-skinned alien being held prisoner inside. Freed, the alien introduces himself as J'onn J'onzz. Before he can tell his story, the trio are confronted by a group of army soldiers. Superman tries to explain, but soon the soldiers morph into white-skinned aliens and aim their weapons at the trio.
On Themyscira, Diana enters the Temple of Athena, and prays her mother's forgiveness. She picks up a set of armor laid at the altar and puts it on...
At the military base, Superman, Batman, and J'onn flee the scene, with their attackers close behind. Taking to the air, they find themselves pursued by swarms of flying craft. Although they manage to down some, the Batwing is critically damaged, and nearly crashes; however, Batman is saved and the fighters are driven off by the timely arrival of four more heroes: Green Lantern/ John Stewart, Hawkgirl of Thanagar, Princess Diana, and the Flash.
J'onn explains: The aliens invaded Mars a thousand years ago, all but wiping out J'onn's people, and absorbing their telepathic and shape-changing abilities. J'onn was the lone survivor of a strike mission that incapacitated the invaders, and he sealed them away in an underground chamber five hundred years ago. Unfortunately, the astronauts released them while J'onn was hibernating. J'onn came to Earth to warn them, but was captured on arrival by the aliens. Instead, he used his partially-blocked telepathic powers to summon the heroes together. Unfortunately, the nerve gas which the Martians used to incapacitate the aliens before is made from a now-extinct Martian plant, and cannot be reproduced.
With their presence on Earth established, the aliens set up enormous factories that project an ionizing field into the atmosphere, creating a cloud cover that shrouds the entire planet. J'onn explains that the invaders are nocturnal, wishing to block out the sun, and the heroes agree that the factories should be investigated and destroyed.
Unused to working together, but resolved, the heroes split into three groups to destroy a factory each. Superman and Hawkgirl head to Metropolis, but are captured. Flash and Green Lantern attack another, but are forced to retreat; J'onn, Diana, and Batman attack a third. While inside, Batman discovers that the aliens are vulnerable to the sun's rays, which is why they are creating the cloud cover. They also manage to steal the crystal powering the factory.
Then the trio is attacked, and J'onn and Diana escape, but Batman, who stays behind to hold them off, is cut off and apparently killed.
The four remaining heroes regroup in Metropolis and prepare to free Hawkgirl and Superman. J'onn warns that they do not have much time, as the Imperium — the leader of the Invaders — will be arriving soon. While Flash creates a diversion, J'onn, Diana, and Green Lantern breach the facility. Managing to fight off the aliens, they find Superman and Hawkgirl in a holding cell, but it's a trap. The two heroes are actually aliens in disguise, and the rest of the heroes are captured.
As the six heroes are held captive, they are shocked to see Senator Carter appear alongside their captors. It turns out that Carter is actually an alien in disguise; the real Carter perished on Mars. Using his persona, the aliens learned as much as possible about Earth's defenses, and also tricked humans into disarming their most powerful weapons.
With no effective obstacles to their invasion left, the aliens signal a mothership orbiting the Earth, and receive their leader, the Imperium. The Imperium remembers J'onn, and begins to torture him. The Imperium calls on J'onn to surrender, saying that he has finally lost, but J'onn lets slip that he still has a plan. Then Batman appears, surprising everyone. J'onn explains that he telepathically shielded Batman from detection until then. Batman has used the time to sabotage the ion crystal, reversing the field's polarity. The clouds part, and the sun shines through the opening in the factory's roof.
Exposed to the sun, the aliens begin to burn and die. Batman explains that the aliens have no resistance to ultraviolet radiation, as he helps to free Diana. Superman, having regained his powers thanks to the sun's yellow light shining through again, frees himself via his heat vision, then frees Hawkgirl, who frees John, then Diana frees Flash. Afterwards, they all engage in combat with the aliens, while smashing large holes in the roof to kill off the remaining aliens. The Imperium, its skin blistering grapples with J'onn, then hastily retreats back into its shuttle, leaving the Carter doppelganger to die, and makes for the mother ship. However, Diana lassoes the shuttle, which Hawkgirl further damages with her mace, and swings it into the factory, destroying both it and the Imperium.
The other heroes quickly evacuate the captured humans being held there, before the factory explodes. The mother ship flees into space.
Earth rejoices over the repulse of the invasion, but several skeptics, including General Wells, warn that they got lucky; if the aliens or a similar threat return, the Earth has no means of advance warning. Watching the report, Batman ponders this remark...
A short time later, the heroes assemble aboard a large space station orbiting the Earth, built and launched in secret by Wayne Enterprises. The station will provide advance warning in case of another invasion.
Superman addresses the assembled heroes, saying that the invasion has proved to him that even he isn't powerful enough to safeguard the Earth by himself. He proposes the formation of the Justice League. Four of the other heroes agree (in his or her own way); Batman, used to operating solo, is reluctant to join a team, but assures them that he'll be on call when they need help. The last holdout is J'onn, who is off by himself, looking out at the stars. When Superman goes to him, J'onn says he is the last surviving member of his race. Superman says he can relate, and assures J'onn that he doesn't have to be alone anymore.
Home Video releases
Justice League: Secret Origins
Justice League: Secret Origins
Justice League - Season One
Justice League: The Complete Series
Justice League Mini-DVD
Justice League - Season One
In the beginning of part II, Superman throws a tank at the Invaders, causing an explosion that is reused footage from Batman Beyond: Return of the Joker, when the console that the Jokerz tried to steal blows up. This is used again in part III, when Hawkgirl administers the final blow to the Imperium mother-ship.
In part II, when one of the Imperium jets crashes in the gorge, footage of the explosion of the Jolly Jack Candy Factory from Batman Beyond: Return of the Joker, is used.
In part III, when Flash gets the first Walker to blow up, the resulting explosion is reused footage from the scene of the Superman: The Animated Series episode "World's Finest" in which one Wayne/Lex T-7 blows up another droid.
Wonder Woman says they have to destroy the "factories" despite never seeing them and wondered what the smoke in the horizon is just prior.
It does not seem plausible that the aliens would entrap Hawkgirl in the substance with her Nth metal mace in her hand.
Superman and Batman last teamed up in the Superman: The Animated Series episode "The Demon Reborn".
Diana's absence from Themyscira ends in "Paradise Lost" when she reluctantly returns after several months with the Justice League.
Superman's dialogue about his hard work in earning the people's trust and General Wells' distrust are references to the Superman: The Animated Series finale "Legacy".
Batman only joins the Justice League as a part-time member, a fact mentioned in the Batman Beyond episode "The Call".