Inside LexCorp, the seven founding members of the Justice League and Amanda Waller have just been treated to the bizarre sight of Brainiac emerging from inside Lex Luthor's body. Brainiac explains that he inserted a microscopic copy of himself into Luthor's body when he was holding Luthor prisoner inside LexCorp years earlier. Since then, he has grown steadily, until Luthor was, for all intents and purposes, acting under his control – as a by-product of his occupancy, Brainiac cured Luthor's Kryptonite poisoning and gave him his mysterious super-strength. The last act Luthor was to accomplish was to transfer Brainiac's consciousness into the "more suitable" android body.
Having had enough exposition, the League attacks, but the Luthor/Brainiac hybrid has not only super-strength, but flight capability, and the ability to convert the building into mechanical constructs, with which he overpowers the League. But J'onn breaks free of their restraints and smashes Brainiac's body. As his final move, Brainiac converts the entire top of the LexCorp tower into an enormous skull-like robot, and attacks again. But the combined power of the League manages to destroy it.
However, the fight was only a diversion. Under Brainiac's control, Luthor is walking along a sewer, to find a place where he can stop and repair himself. Brainiac makes clear that he regards Luthor as only a temporary vessel, which Brainiac will digitize and then destroy, per his programming. Luthor points out that Brainiac's programming is devoid of purpose: its ultimate end is simply for him to digitize, and then destroy the entire universe – after that, nothing. Luthor says he can show Brainiac a higher purpose.
In conference with Waller, the League deduces that since Brainiac's body is entirely nanotechnological now, he will go to Cadmus to harness the power of the Dark Heart. They call for backup, but the League teams on the ground are too far away, and the Watchtower cannot send help – the Javelins were all wrecked in the attack, and the teleporters are still down.
Sure enough, as soon as they arrive, Brainiac has done just that: absorbing the nanotechnology, a new entity is created, a true fusion of Luthor and Brainiac, which has created a machine that will enable him to instantly absorb, and then destroy, all the knowledge stored on Earth, and then the universe – only they will now be able to re-make the universe to their liking.
To fight the League, Brainiac conjures up android replicas of the Justice Lords, each of which confronts its opposite and goads him/her with her worst fears: Superman, the fear in others that his power inspires; Lantern, his heartbreak over Shayera; Shayera, her status as an outcast on both Thanagar and Earth; Flash, his immaturity compared with the rest of the League. They are all resistant to the goading, and defeat their counterparts, and manage to destroy the machine, but Brainiac is still too powerful for them. All of them are knocked unconscious except for Flash. Luthor/Brainiac prepares to kill Flash, but Flash vibrates free of his restraints, and is left standing alone against Luthor/Brainiac.
Luthor/Brainiac taunts, "are you going to fight me, boy?" Flash hesitates, then streaks away. Luthor/Brainiac begins reassembling his machine – and then Flash hurtles at him from the opposite direction, having run so fast that he's circled the globe in only a few seconds, and hitting Luthor with enough force to tear away a chunk of his android armor. Flash makes his fastest run ever, circling the world faster and faster each time, hitting Luthor harder and harder each time. Then he stops, his body crackling with the speed energy he's tapped into, and applies his vibrating hands to Luthor's armor, tearing it completely away, and leaving him naked and helpless at the bottom of a crater.
As the League rises from unconsciousness, Flash stands, unsteady, and then fades completely away, to the others' horror. Luthor manages a weak chuckle: "What do you know? I did kill him."
Now is the moment of truth for Superman: he seizes Luthor, and his eyes glow red... then fade away. At the end of the day, he is not a Justice Lord – no matter how much he wishes he could do what that one did.
Then J'onn shouts that Flash is still alive, he can sense him telepathically. Shayera reaches in the direction J'onn is pointing, and her hand touches a portal to some other dimension, the "Speed Force," into which Flash has been pulled. She seizes his hand, all six of them form a chain, and it takes all their combined strength to pull Flash back. A short distance away, Waller tells The President to call off the air strike against Brainiac.
The next day, Superman addresses a crowd in Metropolis, including the members of the expanded League, the Watchtower support crew, the press, and various citizens. He says the League has been guilty of arrogance, and has alienated the people it was trying to protect. That being the case, the founders have decided to disband the League, and decommission the Watchtower: "This is the end."
In the silence that follows, the founders begin to dismount the stage – and Green Arrow steps forward.
This speech is greeted with applause from the crowd. It is a turning point for Superman: after so many years, he feels he has finally regained the trust he lost when he attacked the earth under Darkseid's control. Bowing to the crowd's pressure, he agrees that the League will stay in service, but they will have to make changes to ensure they remain in touch with the people...
As Superman goes on, Batman excuses himself and throws a verbal wink to Arrow, who has justified Batman's reasons for recruiting him.
That evening at the Daily Planet, Clark Kent drops in on Lois as she is finishing her story on the League. He is surprised to hear that she's using the adjective "ambivalent," and she shoots back that her job is to be as tough on Superman as she is on any subject – but only because he himself has set such high standards. After all, she finishes, "he's only human." Clark smiles.
- The episode picks up directly from the events of "Panic in the Sky."
- Brainiac refers to the events of Superman: The Animated Series, "Ghost in the Machine." According to him, the version of himself that has been developing inside Luthor is separate from the version which Superman destroyed in The New Batman Adventures, "Knight Time," or in Justice League, "Twilight."
- Brainiac also refers to his brief collaboration with, and betrayal by, Darkseid in "Twilight."
- The remains of the Dark Heart reappear after the episode of the same name.
- Luthor/Brainiac refers to Question's pet theory in "Question Authority" that the events of "A Better World" will repeat themselves in their dimension.
- Although Brainiac reappears in three episodes of the final season of Justice League Unlimited, it is unclear whether this version is a hallucination of Luthor's, or some true remnant of the android inside Luthor's body.
- Green Arrow comes full circle; when he was first recruited in "Initiation," he believed the League was too focused on "big" threats for him to be compatible with it; now he sees that the world needs the League, and (unconsciously) shows that the League needs him.
- Although Flash has almost single-handedly saved the world at least once before, in "Eclipsed," it is his actions here that seem to finally earn him the full respect of his teammates, as witness Batman's grudging agreement to show up at the dedication of the Flash Museum in "Flash and Substance."
- The flashback that recreates the scene from Superman: The Animated Series episode "Ghost in the Machine" shows Brainiac blasting Luthor with a yellow beam. However, in the original episode, the beam was blue.
- Batman quotes the famous Latin phrase, "Quis custodiet ipsos custodes," attributed to the Roman poet Juvenal, and variously translated as "Who guards the guardians?" or "Who watches the watchers?" This is a tribute to the Alan Moore comic, "The Watchmen," which grapples with the the darker side and ethical duties of superheroes.
Amanda Waller: I'll be dipped.
Luthor: I'm offering you the one thing you've always lacked. A certain something that I happen to have in abundance.
Android Superman: We've lost their trust. The people are afraid of us. Power corrupts after all, and who has more power than Superman?
Brainiac: I have learned from my encounter with Darkseid that organic beings cannot be trusted.
Superman: I know you're in there somewhere, Lex. Fight him!
Shayera Hol: Less talking, more hitting!
Android Flash: Slacker! Child! Clown! We have no place among the world's greatest heroes.
(Lantern hammers the android version of Hawkgirl)
Superman: I'm not the man who killed President Luthor. Right now, I wish to heaven that I was, but I'm not.
Flash: I can never go that fast again. If I do... I don't think I'm coming back.
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