Batman confronts Amanda Waller for information about her organization. As it happens, one of her associates (Dr. Milo) looks to settle a score against her by releasing Doomsday from captivity. The newly freed Doomsday is more interested in going after Superman, who's in the process of helping the League evacuate the island of San Baquero.
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!!Tropes

* AbortedArc:
** Hugo Strange's cameo was likely to set up an appearance in a later episode, but he was a casualty of the [[ExiledFromContinuity Bat Embargo]]. His role is seemingly replaced by Dr. Moon later in the season.
** According to Bruce Timm in the Season 3 Cadmus Exposed featurette, Batman's doubts about the League were going to ultimately see him switch sides. This was abandoned because the writers couldn't figure out how to do it without making Batman look like a traitor and villain or the League looking like the villains, so Batman's doubts are forgotten about for the rest of the season. This solidifies in "Clash" when Batman notes the situation in that episode was a set-up to make Superman look bad.
* AdaptiveAbility: Doomsday, just like in the comics. For one thing, Superman tries his heat vision to neutralize him like his Justice Lord counterpart did, only for Doomsday to NoSell it.
-->''"Uh-uh-uh. Can't beat me the same way twice."''
* ArsonMurderAndJaywalking:
** Batman telling Waller the things Cadmus wouldn't want to be exposed to the public when she threatens to reveal his identity:
--->'''Batman:''' I'm sure the American people would be just as interested in your activities as mine: secret weapons, illegal cloning experiments, bypassing Congress...
** General Eiling's defense of launching a kryptonite warhead at San Baquero.
--->''"We have to sanction Doomsday, we were gonna get to Superman somewhere down the line, and we've been trying to stop drug traffic from San Baquero for years."''
* ArtEvolution: Downplayed, but Hugo Strange and Dr. Milo's BTAS-era character models have been tweaked and updated for the post-BTAS TimmStyle.
* BackForTheDead: Dr. Milo (unseen since the early days of ''WesternAnimation/BatmanTheAnimatedSeries'') returns for a grisly demise at the hands of Doomsday.
-->'''Waller:''' Milo. I'll have his hide for this.\\
'''Soldier:''' Doomsday beat you to it, Ma'am.
* BewareTheSuperman: Waller's motivation for Cadmus.
* CallBack:
** Amanda Waller says getting Luthor a pardon required Superman telling the government all about [[Recap/JusticeLeagueS2E11And12ABetterWorld the Justice Lords and their world]]. It made certain people wonder what would happen if the Justice League turned evil and led to the full formation of Cadmus.
** Milo references [[WesternAnimation/BatmanTheAnimatedSeries Dr. Kirk Langstrom]], having used his research for Cadmus' purposes (though apparently without much success).
** When the League wonders where Cadmus recived its funding, Batman alludes to [[WesternAnimation/SupermanTheAnimatedSeries Luthor's role in funding General Hardcastle's operations]].
* TheCape: Batman begins to wonder if the superheroes can truly be trusted, but Superman insists he would never go as far as his Justice Lords counterpart. Batman is unmoved.
* CassandraTruth: Despite being told the truth about his purpose by Milo, Doomsday's ''still'' obsessed with wanting to kill Superman instead of the people that used him. Downplayed, as it's less a matter of Doomsday not believing the truth and more that he doesn't care in the least.
* ChekhovsGunman: Unintentionally averted. Hugo Strange makes an appearance as part of Cadmus’ council, seemingly setting him up for a role later on. However, the character being used as the BigBad for WesternAnimation/TheBatman led to him being ExiledFromContinuity and his role given to [[RememberTheNewGuy Dr. Moon]].
* ClothingDamage: Superman's costume is shredded in his fight with Doomsday, with the entire upper body being torn away.
* ConspiracyTheorist: The other founding members recoil at the mere mention of the Question. Batman concedes the guy's wound tight, but still the best man for this particular job.
* ContinuityNod: Batman mentions [[Recap/JusticeLeagueUnlimitedS1E9Ultimatum the Ultimen]] and [[Recap/JusticeLeagueUnlimitedS1E6FearfulSymmetry the clone of Supergirl]] while briefing the other League founders about Cadmus. Hamilton also mentions Galatea, informing the other Cadmus senior members that she's recovering from the injuries she suffered in her debut.
* CrazyPrepared: Eiling's Kryptonite nuke is equipped with magnetic repulsors, which prevent it from being destroyed by conventional missiles (as Batman discovers when he tries to take it down in the climax).
* DarkReprise: When Superman throws Doomsday into the volcano, we get one of these to the theme from ''WesternAnimation/SupermanTheAnimatedSeries''.
* EveryoneHasStandards: Waller is outraged that Eiling would launch a warhead at both an island full of innocent people and Superman unprovoked.
* EvilIsNotAToy: Milo releasing Doomsday backfires on him pretty much instantly.
* EvilIsPetty: Milo's response to being demoted is to release Doomsday to murder Waller and Hamilton.
* ExactWords: Doomsday agrees to solve Dr. Milo's problem.
-->'''Dr. Milo:''' What are you--?\\
'''Doomsday:''' [[PreMortemOneLiner Your problem's solved.]]\\
''[Milo screams]''
* FanDisservice: The handsome and muscular Superman gets a shirtless scene...while being beaten half to death by Doomsday.
* TheFarmerAndTheViper: In exchange for being freed, Doomsday kills Milo.
* FatalFlaw: Dr. Milo's desire for revenge against his peers gets him killed.
* FauxAffablyEvil: Doomsday, of all people, takes a moment to sarcastically greet Superman before attacking him.
-->'''Doomsday''': Superman. I've come to kill you. Is this a bad time?
* {{Foreshadowing}}:
** Hamilton mentions that Galatea is almost ready to return to active duty.
** Luthor's presidential campaign is in full swing and will recur throughout the season.
** Batman says he has the Question looking into any connection between Luthor and Cadmus--setting up parts of "[[Recap/JusticeLeagueUnlimitedS2E6DoubleDate Double Date]]" and "[[Recap/JusticeLeagueUnlimitedS2E9QuestionAuthority Question Authority]]".
* FreudianExcuse: Dr. Milo explains to Doomsday that he was conditioned to instinctively hate Superman and try to kill him. Doomsday pointedly doesn't care.
* GodzillaThreshold: Superman's fight with Doomsday goes so poorly that the Man of Steel makes a desperate attempt to lobotomize the monster, just like Lord Superman did ([[AdaptiveAbility with no success]]), and resorts to sending Doomsday to the Phantom Zone to end his threat without killing him.
* GoryDiscretionShot: The audience only hears Milo's scream of terror as Doomsday kills him. Judging from the reaction of a Cadmus soldier, what was left of Milo wasn't pretty.
* TheHeart: Discussed. Flash insists that the Justice Lords only went nuts because their Flash died, so he suggests the team focus on keeping him alive and that everything will thus be fine. The other six are less convinced.
-->'''J'onn:''' [[DeadpanSnarker Let's put a pin in that theory to explore another time.]]
* IDidWhatIHadToDo:
-->'''Superman:''' He left us no choice.\\
'''Batman:''' Spoken like a true Justice Lord.
* KillMeNowOrForeverStayYourHand: When the Justice League decides to banish Doomsday to the Phantom Zone, Doomsday tells them that killing him would have been a better option.
* IndulgentFantasySegue: After Waller reassigns him, Milo fantasizes about pulling out a blaster and shooting her.
* KnightTemplar: Amanda Waller sees herself as a patriot defending the world from a team of superheroes that answer to no one.
* LaserGuidedTykebomb: Doomsday. Even after having it explained to him that his hatred of Superman was manufactured, and that the version he fought was an EvilTwin, he's still totally focused on killing him.
-->'''Doomsday:''' Superman is Superman, and I ''will'' kill you.\\
'''Superman:''' Why?!\\
'''Doomsday:''' It's who I am. I don't care "why".
* MisplacedRetribution: {{Averted|Trope}}. Even though Milo explains to Doomsday that he was conditioned to kill Superman by Cadmus, and the Man of Steel tries to tell him that he wasn't the one who lobotomized him, Doomsday makes it clear that he doesn't care about any of that and just wants to kill Superman.
* TheNeedsOfTheMany: Superman tells Wonder Woman to stay with the evacuation rather than help him fight Doomsday. "This isn't important. Getting those people to safety is."
* NoHoldsBarredBeatdown: Doomsday clobbers Superman for much of the episode, but the Man of Steel reverses it in the end.
* NotSoDifferentRemark: Batman begins to wonder if the Justice League is going down the same path as the Justice Lords, starting with Luthor running for president.
* NotMeThisTime: Played with. Batman hacks into Waller’s line with the President to tell her to call off the nuke launched at San Baquero. She isn’t aware that Eiling launched the missile but plays it off like she did before hanging up to go yell at Eiling and try to abort the launch. Batman presumably picked up on the tone in her voice and notes, “She didn’t know...”
* NotSoStoic: Despite successfully staring down Batman in his confrontation with her, Waller's hand is still shaking slightly when she sounds the alarm. Also Batman himself, who goes off on Superman for the unilateral decision to exile Doomsday for all but proving Waller right. See WhatTheHellHero for more.
* OhCrap: Waller answers a phone that only the President has the number to, but it's Batman on the other end. Happens again when he tells her about the missile.
* PowerFantasy: Milo's aforementioned fantasy of shooting and killing the rest of his Cadmus associates.
* PreAsskickingOneLiner: "Then I guess I'll need a bigger fire."
* TheReveal:
** Waller and Hamilton's organization is Cadmus, with General Eiling from "[[Recap/JusticeLeagueUnlimitedS1E10DarkHeart Dark Heart]]" being among the department heads. Also on hand are Tala, Hugo Strange, and Dr. Milo.
** Doomsday's out of nowhere appearance in "[[Recap/JusticeLeagueS2E11And12ABetterWorld A Better World]]" is explained by him being developed as an anti-Superman weapon that grew too powerful to control.
* {{Retcon}}: In his last appearance, Doomsday appeared to be an alien monster who, in his own words, wanted to see the best Earth had to offer. Here, he's somewhat awkwardly retconned into a failed anti-Superman weapon, even though he voiced no special interest in Lord Superman last time.
* RevengeBeforeReason: Doomsday is well aware that the Superman he attacks isn't the one who lobotomized him, and is even told by Milo that his hatred of Superman was programmed and conditioned. Doomsday doesn't care about either fact; he just hates Superman and is single-mindedly focused on his death.
* RewardedAsATraitorDeserves: Milo tries to overthrow Cadmus by releasing Doomsday and telling the latter his hatred against Superman was programmed into him. Instead of trying to exact revenge on those who conditioned him, Doomsday kills Milo and goes after Superman.
* RoaringRampageOfRevenge: Defied on two counts. Milo releases Doomsday in the hopes of this happening to Waller and Hamilton, but only he gets killed. Later, Doomsday demonstrates he's not really seeking to avenge his earlier lobotomy; he's just trying to kill Superman because that's all he cares about.
-->'''Eiling:''' Doomsday went straight for Superman. I love a well-conditioned soldier.
* ShirtlessScene: Superman loses his shirt to ClothingDamage while fighting Doomsday.
* VillainHasAPoint: When it's all over, even Batman concedes Waller has every right to be cautious around a growing team of superpowered individuals, even if they saved the Earth and beyond countless times.
-->'''Batman:''' Whatever you think you're doing, if you present a threat to the world, the Justice League will take you down.\\
'''Waller:''' If ''we'' present a threat?! You've got a spaceship floating over our heads with a laser weapon pointing down! In another dimension, ''seven'' of you overthrew the government and assassinated the President! ''We're'' the good guys, protecting our country from a very real threat: ''You''.
* WhatTheHellHero: The Justice League founders decide to send Doomsday into the Phantom Zone instead of finding a way to kill him. A recovering Batman later learns about this and, following his conversations with Waller during the episode, has this exchange with Superman after the Man of Steel claims [[IDidWhatIHadToDo the monster left them no choice]]:
-->'''Batman:''' What if Luthor does become President, like he did in their world? What would stop you from doing what ''that'' Superman did?\\
'''Superman:''' There's always that Kryptonite you carry around.\\
'''Batman:''' '''''You don't get to joke!''''' Not today. I just [[TakingTheBullet took a bullet]] for you.\\
'''Superman:''' I'm sorry, Bruce. You're right. But you don't have to worry about the Justice League. Trust me. You know me.\\
'''Batman:''' Yeah, I do.
* WhatWereYouThinking: Spoken verbatim by Waller to Eiling when she confronts the latter over launching a nuke at San Baquero.
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