Two astronauts explore an underground cavern on Mars, when one of them, J. Allen Carter, stumbles onto a large ornate door. As he forces it open, something rushes out, reaching towards him...
Two years later, Batman spies on a satellite communications facility operated by Wayne Tech and catches three employees tampering the equipment. He is taken by surprise by them, as they are not human to begin with. However, Superman arrives and forces the employees to flee. Before he and Batman can deal with them, Superman sees strange images in his mind and is rendered temporarily unconscious. The two heroes later discuss what happened in which Batman explains that this station is the latest in a series of events 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.
Meanwhile, J. Allen Carter is now a U.S. Senator and making headway for boldly proposing the world into 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. 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 he is attacked by a alien guard dog and forces him to contact Superman. 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 war machine appears, and begins attacking. Superman and Batman throw their efforts in subduing the war machine, but more meteors containing similar machines begins landing all around the Earth.
While preparing to fight again, Superman suffers another psychic migraine; entranced, he flies away. 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 shapeshift into white-skinned aliens. The three are forced to run, but are pursued. Fortunately, they are assisted by the timely arrival of four more heroes: Green Lantern John Stewart, Hawkgirl of Thanagar, Wonder Woman, and the Flash. All these heroes were also summoned by J'onn J'onzz, who explains that the white aliens, the Imperium, invaded his home planet Mars thousands of years ago and all but wiped out J'onn's people. 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 until the astronauts released them while J'onn was hibernating. J'onn came to Earth to warn them, but was captured on arrival by the Imperium. Instead, he used his partially-blocked telepathic powers to summon the heroes together.
With their presence established, the Imperium are using factories that project an ionizing field into the atmosphere, creating a cloud cover that shrouds the entire planet from the sun, as J'onn explains that the invaders are nocturnal. The heroes agree that the factories should be investigated and destroyed, which they are split into three groups. But during one incursion, the group consisting of Batman, Wonder Woman, and J'onn discovers that the Imperium are fatally vulnerable to the sun's ultraviolet rays. Unfortunately, Batman is apparently killed by the aliens as he tries to hold them off. Meanwhile, Superman and Hawkgirl are captured by the Imperium.
The remaining heroes gather in Metropolis to rescue Superman and Hawkgirl as J'onn warns that the leader of the Imperium will be arriving to Earth soon. The heroes infiltrate the facility holding Superman and Hawkgirl, but are caught in a trap. The six heroes are held captive and are shocked to see Senator Carter appear alongside their captors. Carter is actually an alien in disguise while 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, who then begins torturing J'onn to demand his surrender for having lost everything. 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 Imperium's machines and reversing the field's polarity, exposing the Imperium to the sun. The heroes are then freed and engage the aliens while the Imperium leader hastily retreats to the mothership while leaving the Carter doppelganger to die. However, Wonder Woman lassoes the shuttle carrying the Imperium leader, which Hawkgirl further damages with her mace, and swings it into the factory, destroying both it and the Imperium. With their plans thwarted, the remaining forces of the Imperium flees into space.
Earth rejoices over the repulse of the invasion, but several skeptics stated that they are only lucky and are certain that the Imperium or a similar threat will return. A short time later, the heroes assemble aboard a large space station orbiting the Earth, built and launched in secret by Wayne Enterprises. Batman has the station to 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.
- Alien Invasion: The episode features one and the Justice League managed to stop it.
- Arc Villain: The Imperium serves the role as this for this three-part pilot.
- Big "NO!": This is said by Wonder Woman when Batman appears to die.
- Blood Knight: Wonder Woman and Hawkgirl are most eager and willing to become involved in fights with the Imperium.
- Body Horror: The leader of the Imperium snakes a tentacle under the skin of J'onn's face.
- Casanova Wannabe: The Flash immediately puts his arm on Wonder Woman, much to her shock.Flash: "Dibs on the Amazon!"
- Superman calling Batman "Bruce" is due to his knowledge of his identity, which he learned back in the Superman: The Animated Series episode "World's Finest".
- Also, Superman's dialogue about his hard work in earning the people's trust and General Wells' distrust of him can be seen as references to "Legacy".
- Call-Forward: Batman states that he only joins the League as a part-timer; this fact was first mentioned in the Batman Beyond episode "The Call", which aired a year earlier.
- Dead Person Impersonation: The astronaut J. Allen Carter never made it back to Earth, and one of the shape-shifting aliens impersonates him, and becomes Senator.
- Door Jam: Batman is trapped (and apparently killed) when a portal closes before he can follow Wonder Woman and Martian Manhunter.
- Dying Like Animals: Wonder Woman isn't impressed seeing people looting, but Humans Are Bastards is averted when we see two people trying to free trapped children, helped by Green Lantern.
- Everyone Meets Everyone: Some of the Leaguers had worked together before, or knew each other by reputation, but this is their first time together as a full group. Superman is so impressed by what they achieve together that he suggests making it permanent via forming a team.
- Faking the Dead: J'onn helps Batman do this by making Wonder Woman believe he was killed, so that he can mentally shield him and allow him to prepare the countermeasure against the Imperium - presumably he read his mind and was thus aware of the plan (including the Weaksauce Weakness of the invaders).
- Hoist by His Own Petard
- Hollywood Science: The Martian commando team is shown wearing gasmasks against the nerve gas. Nerve agents are absorbed through the skin as well as through breathing.
- Though whether this applies to Martians who can say.
- It Only Works Once: Justified. After hearing J'onn's story, Flash asks him why he doesn't make another batch of the nerve gas he used the first time he stopped the Imperium. J'onn explains that the gas can only be made by a rare Martian plant, and the only sample he brought with him was destroyed upon his capture.
- Leeroy Jenkins: Flash charges in, ignoring GL's attempt to plan things first. Naturally he gets stuck (literally).
- Mythology Gag:
- Secret Origins was a comic book series that retold the origin stories of DC superheroes.
- The story begins with a man named J. Allen Carter. In the comics, the story of the Justice League arguably begins with the Justice Society, whose founder members included the original Flash, Green Lantern and Hawkman: Jay Garrick, Alan Scott, and Carter Hall.
- When Superman suggests forming a team of heroes, the Flash responds, "What, you mean like a bunch of Super Friends?"
- Noodle Incident: Batman isn't surprised to see Hawkgirl, just to see Hawkgirl at the fight. Superman doesn't ask Green Lantern John Stewart where Green Lantern Kyle Rayner, the Green Lantern he met in his own show, is.
- Nuclear Option: Discussed and prevented. Superman got the UN to let him dismantling all the world's nukes... only for the Earth to be immediately invaded by aliens after humans no longer had a Nuclear Option (one of the major supporters for the move was an alien pretending to be human). Later episodes had nuclear weapons, so most likely they rebuilt them to ward off more alien invasions.
- Perception Filter: J'onn making Batman invisible through his mental powers.
- Plot Hole: The aliens are burned by sunlight, even those disguised as humans. How could the alien impersonating Carter have come back to Earth and spent two years as a senator without ever stepping foot in sunlight?
- Reverse Polarity: What Batman does to the Power Crystal he got his hands on.
- Apart from all the ones to The War of the Worlds listed below, there are a couple to John Carter of Mars. The two astronauts in the beginning are named Ed (As in Edgar Rice Burroughs) and Carter, whom we later find out is named J. Allan Carter (J for John, perhaps?)
- There is also a small one to a certain rival superhero team. Senator Carter mockingly calls the team "Earth's Mightiest Heroes", a term usually reserved for The Avengers.
- Sole Survivor: J'onn J'onz is the last Martian.
- Stock Scream: The Wilhelm Scream when J'onn throws an invader off the power core.
- Three Episode Pilot: Secret Origins is this.
- Take That!: The entire premise of aliens having Superman destroy nukes could be seen as a Reality Ensues ending for Superman IV: The Quest for Peace... If reality had alien invaders as an option.
- Tentacled Terror: The "Imperium" is a very evil, big, night-loving blob with creepy tentacles.
- Time Skip: Two years pass between the Cold Open (where the real Carter accidentally releases the Imperium) and the present day. It's also presented that an (unspecified) measure of time has passed since "Legacy" as Superman has managed to repair the people's trust in him to some degree (whereas they seemed to near-universally distrust him after that).
- Tripod Terror: As you'd expect with invaders from Mars. Turns out this makes them vulnerable to being tripped up.
- Weakened by the Light: The Imperium has no resistance to sunlight.
- Where Does He Get All Those Wonderful Toys?: Superman asks Batman if his stockholders know about the newly-commissioned Watchtower, which Batman handwaves with "hidden as a line item in the Space R&D budget." Sure, that hides the funding, but says nothing about assembly either pre-launch or in orbit. (Although with Superman available, Batman at least wouldn't need a launch vehicle or if Clark had a spare weekend, a construction crew.)
- On the other hand Superman seems impressed by the Watchtower, as if he's seeing it for the first time.
- Whole Plot Reference:
- The entire episode is based on The War of the Worlds. Both are about alien invaders from Mars who want to sap the world's resources, both feature tripod crafts that level major cities, and when it seems the aliens have won, they are shown to be easily defeated due to a Weaksauce Weakness set up as a Chekhov's Gun in the first act. There is even a General Wells.
- There's also a Whole Sub-Plot Reference to Superman IV: The Quest for Peace. Superman (recruited by Senator Carter) goes before the United Nations with a plan to personally disarm the world of its nuclear weapons in an attempt at lasting peace. Unlike in the movie, however, it's a trap.