Upon receiving the message, the League announce that they're locking up the Legion. As several prepare to fight back, an emergency message arrives: Around the world, boom tubes open, and the Apokoliptian fleet appears, releasing Parademons and ground troops on the helpless masses. The Legion insists that they be allowed to fight alongside the League; they may be criminals, but Earth is their home too. Batman agrees, saying that the League needs all the help they can get. Superman and Wonder Woman are more skeptical, but Luthor announces that he isn't saving Earth: as far as he's concerned, both the Justice League and the Legion of Doom are little more than tools to help him achieve revenge on Darkseid for taking Brainiac away. Once the invasion is dealt with, it will be "back to business as usual". Superman reluctantly goes along, but Wonder Woman orders that the villains fight in mixed teams.
Mr. Terrific, handling central command from the Watchtower, sends out an "Omega-level alert" to the entire League: around the world, various Leaguers prepare for battle and are teleported away. Battle erupts everywhere, with the allied heroes and villains defeating legions of Darkseid's forces around the World.
Superman, Batman, and Luthor confront Darkseid at his command ship, which Batman deduces is the best-protected one, hovering over the Daily Planet building in Metropolis. Emerging from his ship in a beam of light, Darkseid tells Superman that he intends to make the Kryptonian suffer by watching his adopted world die before killing him. His speech ends with the same phrase Superman told him before their previous standoff: "Let's go".
As the battle progresses, the Apokoliptian forces set up huge drilling machines designed to dig holes straight through to the Earth's core, creating fire pits that will make Earth another Apokolips. Mr. Terrific orders them taken out at all costs, and the Leaguers destroy several, though Shayera is badly wounded from a Parademon spear.
Over the Great Wall of China, a middle-aged Asian man tells his wife to find cover, then reveals himself to be J'onn J'onzz, who joins Wonder Woman, Star Sapphire, Vigilante, and Shining Knight in battling Darkseid's Parademons, as they are having considerable difficulty.
In Metropolis, the clash between Superman and Darkseid has destroyed much of the Planet's structure, while Luthor and Batman hold off Parademons. Suddenly, Luthor spots Metron and accuses him of knowing that exactly this would happen. The time traveler states that this outcome was one of the many possibilities that could've resulted from Luthor's rash actions. Luthor demands that Metron help him defeat Darkseid, pointing out that if he knows so much about the Apokoliptian despot that there must be a way to beat him. Metron confesses that there is only one possible solution, but warns that it's too risky. Luthor, raising his gun, does not care. Conceding to his wishes, Metron takes him to the Source Wall, beyond which contains the only thing that could stop Darkseid. Metron warns that only a "twelfth level intellect" could survive the journey through the wall, but Luthor only claims "then I'm overqualified". Luthor flies through an opening in the wall, sees a great light...and screams.
On Earth, Darkseid appears to be winning, but Batman repeatedly interrupts the tyrant's attempts to kill Superman. Darkseid is astonished that a mere mortal would dare to strike him-and even more so when Batman actually evades his deadly Omega Beams, causing them to strike a Parademon, Darkseid claims this is the first time someone has avoided his Omega Beams. He prepares to kill Batman the old-fashioned way, but Superman, who now has his second wind, knocks Darkseid through the wall.
For the first time since their acquaintance, Darkseid is uncertain, maybe even a little afraid, as Superman approaches he explains to the New God that he's always careful about the use of his powers in case he hurts someone by accident, Darkseid however is strong enough to take it all without killing him, so for once, Superman can unleash his full power, which he does by delivering a single, earth-shattering punch that sends Darkseid flying into the air and through several skyscrapers. With his speed, Superman is waiting for him at the other end, and knocks him to the ground with a two-handed blow, creating a crater.
Deciding that he's wasted enough time in hand-to-hand combat, Darkseid traps Superman in a powerful torture field called the Agony Matrix, which activates every pain receptor in the body. While Superman lies helpless, Darkseid claims he will show mercy, and draws a knife with a Kryptonite blade, intending to cut out Superman's heart. Then Luthor appears, having returned from the dimension Metron transported him to, and holding the only thing in the universe Darkseid wants: the Anti-Life Equation. Entranced, Darkseid takes hold of it, and Superman is freed from the Agony Matrix. With Batman, Superman leaves the crater, while Darkseid and Luthor disappear in a blaze of light.
With Darkseid apparently gone, the invading forces from Apokolips retreat from Earth. The Justice League speculate over what happened, and if Darkseid and Luthor had died (most believe they did not). J'onn J'onzz reminds that if they do come back, the League will be ready for them.
With the threat gone, Wonder Woman announces that it is time for the villains to go back to jail. Atomic Skull objects, saying they helped the League save the world. Batman agrees...and gives them a five-minute head start. When the League makes it clear that concession is all they are offering, the Legion turns and runs (although Giganta takes a moment to kiss the Flash).
J'onn calls his wife to tell her he will be back in time for dinner. Superman playfully chides Batman that the five-minute head start shows he is getting soft. With a smile, Batman counters "Don't you have a tall building to go leap?" Wonder Woman, who is walking with both Superman and Batman muses "and the adventure continues..."
Descending the steps of the Metro Tower, the entire expanded League sets off after the villains.
- Darkseid's invasion of Earth in this episode marks the fourth world-wide alien invasion of the Earth in the DC Animated Universe. The prior instances consisted of Darkseid's initial invasion in "Legacy;" the Imperium Invasion depicted in "Secret Origins;" and the Thanagarian invasion depicted in "Starcrossed".
- This episode makes the second time Darkseid tried to create Apokolips on Earth. The first time was Apokolips... Now!
- Both Darkseid and Superman recollect their last encounter in Justice League episode, "Twilight, Part II" (from their different perspectives).
- According to Dwayne McDuffie, Darkseid and Luthor became part of the Source Wall, like everyone else who solved the Anti-Life Equation.
- Back in "To Another Shore", J'onn J'onzz left the Watchtower to live among earthlings in hopes of finding some way to connect with humanity. This episode revealed J'onn accomplished his mission on a level that even shocked his teammates. Not only did J'onn find a new mate on earth, his speech patterns became noticeably much more "human," even while battling in his Martian Manhunter form.
- Orion appears at the end of "Alive!" as one of the heroes confronting the Legion, but in the recap at the beginning of this episode, he has been removed from the picture, and is not to be seen at all in the story. When the scene is shown in the closing cr s, he appears again in the group.
- S.T.R.I.P.E. was in the lineup of heroes that rushed outside the Metro Tower in "Alive!", but in this episode he is teleported with Stargirl from a loft. It is possible that he could've gone to get her, however.
- As she leaves the Metro Tower, instead of holding her Cosmic Staff, Stargirl is seen clearly holding one of the spears of the Parademons. In fact, she is not seen holding her Staff at all this episode, and fights only unarmed.
- Two inconsistencies occur in the battle Shayera takes part in: 1) During the opening shot, it is night but when it cuts to Shayera, it is day, and 2) this battle takes place in Washington D.C. and yet from the Watchtower, the monitor displays New York.
- Darkseid states that Batman is the first to dodge his Omega Beam. However, in the earlier episode "Twilight, Part II", Superman manages to avoid being hit by Darkseid's Omega Beam before engaging in the physical fight with the villain. On the other hand, the Omega Beams merely flew past Superman and didn't move around to follow him, so Darkseid probably wasn't trying to hit him as much as getting into the physical fight. In that case, Darkseid could mean that Batman is the first being to ever dodge the Omega Beams when Darkseid is actively trying to hit his target.
- Lex Luthor's line "we found ourselves dependent on the kindness of strangers" echoes a famous quote from Tennessee Williams's play A Streetcar Named Desire.
- Darkseid's speech about what will happen before he finally ends Superman's life mirrors Superman's speech on "Twilight" about not stopping until Darkseid's a greasy smear on his fist. Both speeches end with "Let's go".
- Order of Battle:
- Metropolis: Superman, Batman, and Lex Luthor vs. Darkseid
- Washington, D.C.: Shayera Hol, Commander Steel, and Atomic Skull
- Paris: Green Lantern, Flash, and Giganta
- Great Wall of China: Wonder Woman, Shining Knight, Vigilante, and Star Sapphire, joined later by J'onn J'onzz
- Rome: Doctor Light, Green Arrow, Black Canary, and Bizarro
- Tokyo: Sinestro, Steel, and Blue Devil
- Unknown City: Hawk and Dove, The Creeper, The Question, and Captain Atom
- Unknown Mountainous Location: Zatanna and Volcana
- Cairo: Toyman
- London: Hawkman, Stargirl and S.T.R.I.P.E.
- Venice: Killer Frost
- Commander Steel saves Shayera by picking up a Parademon's shield and throwing it spinning through the air, in a nod to Marvel Comics' Captain America, whom he resembles. Both heroes have American flag themed costumes. Both obtained their abilities by scientific means during wartime. However Steel's publication origins predate Captain America by 2 years (1939)
- Shayera's wing is impaled by a Parademon's spear, resembling how Angel (another Marvel hero) had his wings originally crippled.
- During the "call to arms" sequence where Leaguers across the globe suited up for transport, Ice briefly "hibernated," encasing herself in a block of ice, then breaking free to reveal herself in costume, powered-up and ready for action. Movement-for-movement, this was the exactly same method of transformation Bobby Drake used to turn into Iceman on the 80s superhero show Spider-Man and His Amazing Friends.
- Each major invasion of Earth that has taken place throughout the series has a similar goal of building a weapon that can destroy the planet. For example, Darkseid's goal of creating "Apocalypse on Earth" using drills refers back to the very first episode, "Secret Origins", where the Imperium's goal is creating darkness on Earth using drills of their own. Another reference is when the Thanagarians try to destroy the Earth by using a hyperspace bypass. Every attempt, of course, failed thanks to the Justice League.
- Batman evades Darkseid's Omega Beams until they hit a Parademon, prompting him to state that no one had ever avoided the Omega Beams; in the Final Crisis story arc of the comics, Batman is seemingly killed by Darkseid's very Omega Beams. Also, minutes after, the Flashes (Barry Allen and Wally West) manage to outrun both the Omega Beams and the Black Racer by vibrating through Dan Turpin's body, thus making the beams hit him and expel Darkseid's essence from the body.
- The second to last line of the episode, and therefore, the DC Animated Universe, is said by Batman. This mirrors the blimp pilot (who, like Batman, is voiced by Kevin Conroy) from the Batman: The Animated Series(and DCAU) premiere episode, "On Leather Wings", voicing the second line of the episode.
- Batman's line "Don't you have a tall building to go leap?" to Superman is a reference to the opening narration of the Fleischer cartoons of the 1940s.
- In the final scene, the Justice Leaguers run down the stairs of the Metro Tower or fly off in groups, which are nods to the DC Comics:
- Batman being the last one seen is a nod to the DC Animated Universe having started with Batman: The Animated Series.
- Writer Matt Wayne had stated the if Justice League Unlimited would have been renewed for another season, he would have liked to write more episodes focusing on Superman and Wonder Woman.