Amanda Waller wakes up and tunes into the news of Lex Luthor announcing he's running for President. Then Batman pays her a visit and after riposting over each other's secrets, Waller notes that the government is concerned over the Justice League potentially going rogue after reports of the "Justice Lords." Now, with Cadmus, Waller and her people believe they have the technology to stop the League "if necessary." Batman departs, while up on the Watchtower, the core Leaguers discuss the matter. On Earth, Professor Hamilton is discussing the success of Cadmus with Tala, General Eiling, Dr. Hugo Strange, and Dr. Milo.
The League suspect Luthor is financing Cadmus while Milo is "retired" from the project after his failure on the Langstrom project. Milo confronts Doomsday, who has recovered from his lobotomy procedure at the hands of the Justice Lord's Superman. He was a genetic creation made out of Kryptonian DNA who was launched into space – when he crashed back down he sought out Superman, which led to the events seen in "A Better World." Milo releases Doomsday to get revenge on Waller, but Doomsday isn't interested and kills Milo and then escapes.
On the island of San Baquero, the League are conducting an island evacuation near an active volcano and Superman is trying to relieve the pressure when Doomsday arrives and attacks. Doomsday partially blinds Superman to negate his heat vision, while Waller orders Eiling to stop Doomsday. The general orders a submarine to launch a nuclear missile lined with kryptonite at the island and Superman orders the others to continue while he fights Doomsday.
Aboard the Watchtower, Batman and J'onn pick up the missile launch and Batman calls Waller to order her to abort the missile. With no one else available, Batman takes a Javelin to intercept the missile despite the danger from re-entry. Waller confronts Eiling, who can't stop the missile which is on automatic. As Superman and Doomsday knock each other free of the volcano and take their battle outside, Wonder Woman goes for Superman and Batman manages to intercept the missile but its protected against missiles. Batman charges the hull with an opposing charge against the missile's magnetic repulsor and manages to take it off-course and into the ocean, ejecting just barely in time.
As tidal waves from the detonation overwhelm the island, the evacuation ships lift off. A nearly-beaten Superman recovers his heat vision and blasts free. He throws Doomsday directly into the caldera of the volcano, setting off the eruption. Wonder Woman rescues the wounded Superman just in time as the island goes up.
The League confront a restrained Doomsday, who is immune to telepathy. Doomsday refuses to implicate Cadmus so Superman uses his Phantom Zone projector to banish Doomsday. Bruce is recovering in the medlab, and is not happy with how Superman handled the matter and begins to believe Waller's fears are warranted. Batman is left to recover as the vision of Lex Luthor as President hangs over them all.
Dr. Achilles Milo first appeared in the comics in Detective Comics #247 (Sept. 1957). A renowned chemist who turned to crime, Milo used a variety of chemical- and medical-related schemes to get at Batman. He was later exposed to chemicals that drove him insane and spent some time in Arkham. Batman consulted him on at least one occasion when he needed chemical expertise.
In the WB animated universe, Milo was introduced in Batman: The Animated Series, in the episode "Cat Scratch Fever." Little was revealed of his origin but his basic profession of chemical and genetic tampering was the same. He appeared in "Moon of the Wolf" where he was the one who made an enhancement chemical for athlete Anthony Romulus that turned him into a werewolf. This is his first appearance in Justice League Unlimited.
Professor Hugo Strange
The bald guy on the Cadmus council appears to be Professor Hugo Strange, who first appeared in the comics in Detective Comics #36 (Feb. 1940). Strange was a psychiatrist and chemist who went up against Batman, In his second appearance a month or two later, he created 10-tall man-monsters which Batman pretty brutally slaughtered in one of the Dark Knight's last portrayals as a killer-vigilante. Strange apparently fell to his death. Strange returned decades later obsessed with determining Batman's secret identity and taking it for himself. He managed to do so, but after a failed attempt to sell it to the Batman's opponents, tried to take on the Wayne identity himself.
In the WB animated universe, Strange was introduced in Batman: The Animated Series, in the episode "The Strange Secret of Bruce Wayne." Little was revealed of his origin but his basic profession of psychiatrist and his obsession with Batman's secret ID were the same. He developed a machine that could read surface thoughts and determined that Bruce Wayne was Batman, but when he tried to sell the secret to other Batman villains, Batman switched tapes and had Robin dress as Bruce Wayne to discredit him. He was put in jail and hasn't been seen since - assuming the character is Dr. Strange, this is his first appearance in Justice League Unlimited.
Tala (the black-haired woman on the Cadmus council) first appeared in the comics in Phantom Stranger vol. 2 #4 (Nov. 1969), and was created by Robert Kanigher and Neal Adams. She has been described as a demoness, a Queen of Hell, and a powerful sorceress. She is a primary opponent of the Phantom Stranger, a mystic wanderer and sometime-League member, and occasionally takes on other heroes of the DC universe. Her powers are great and mystically oriented, and primarily concerned with casting spells and mystic blasts. This is her first appearance in Justice League Unlimited, and her origin here may be substantially different as the comic book version wouldn't be very interest in a government conspiracy. This is her first appearance in the WB animated universe.