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 surprise by them, as they are not human to begin with. However, Superman arrives and forces the employees 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 on what happened in which 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.

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 wiping 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 agrees hat the factories should be investigated and destroyed, which they are split into three groups. But during one incursion, the group consisting Batman, Wonder Woman, and J'onn discovers that the Imperium are fatal to the sun's ultraviolet rays. Unfortunately, Batman is apparently killed by the aliens as he tried 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 [[ReversePolarity 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.

* AlienInvasion
* ContinuityNod:
** Superman calling Batman "Bruce" is due to his knowledge of his identity, which he learned in the ''WesternAnimation/SupermanTheAnimatedSeries'' 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".
** Batman states that he only joins the League as a part-timer; this fact was first mentioned in the ''WesternAnimation/BatmanBeyond'' episode "The Call", which aired a year earlier.
* MythologyGag: When Superman suggests forming a team of heroes. The Flash responds, "What, you mean like a bunch of...SuperFriends?"
* NuclearOption: 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 supports for the move was an alien pretending to be human). Later episodes had nuclear weapons, so most likely they rebuilt the to ward off more alien invasions.
* StockScream: The Wilhelm Scream when J'onn throws an invader off the power core.
* [[FiveEpisodePilot Three Episode Pilot]]
* TripodTerror
* WeakenedByTheLight: The Imperium has no resistance to sunlight.
* WhereDoesHeGetAllThoseWonderfulToys: 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.)
* WholePlotReference: The entire episode is based on ''Literature/TheWarOfTheWorlds.'' Both are about alien invaders from Mars who want to sap the world's resources, both feature [[TripodTerror tripod crafts]] that level major cities, and when things seem the aliens have won, they are shown to be easily defeated due to a WeaksauceWeakness set up as a ChekhovsGun in the first act. There is even a General [[Creator/HGWells Wells]].