In Justice League Unlimited, the DCAU presents Doomsday as a Superman clone. This differs from the comic version where Doomsday is actually a clone from Krypton, by scientist Bertron. In Justice League Unlimited, Doomsday is a Superman clone from STAR LABS by Emil Hamilton, Superman's foremost scientist and traitor. Doomsday, in the episode "Doomsday Sanction," is revealed to have been cloned in order to hate Superman. Geneticist scientist, Dr. Milo, frees Doomsday in order to get revenge on Amanda Waller and Emil Hamilton, only to get killed by Doomsday.
In the Justice League Unlimited show, there are constants. One constant is that Superman is confronted with always bigger physical threats. The other constant is that Superman and the Justice League Unlimited's credibility are always in question. Another thread that runs through the show, however, is that the Justice League Unlimited is creating fear and animosity over a climate of excessive power, foremost of which, is Superman.
Doomsday, presents as the perfect foil since he presents a threat that Superman cannot solve with physical power alone. What the episode shows is that, conquering Doomsday in physical combat is not sufficient, he actually has to be disposed of with advanced Kryptonian technology, namely, the Phantom Zone projector. This is a sanction that is passed in the Fortress of Solitude in the presence of the Justice League Unlimited by Superman; Batman having sacrificed his body, "I took a bullet for you!"
Doomsday is the problem of maximum physical might in combat, and proves that the only solution to ending the threat is only death by Kryptonite missile or battle field removal by the Phantom Zone projector. Doomsday acts as a deterrent to the threat of Superman going rogue for the end of the superpowered warfare between the US government and the Justice League Unlimited.
Doomsday is the ultimate test of Superman and the proof of his limits to physical might. In the fight against Doomsday, Superman is taken to his limits and only conquers by surrendering to an almost animalistic behavior. The problem that Doomsday poses is that of unlimited military power and of the threat of totalitarian government under the form of the Justice Lords.
It is a reminder that the temptation to absolute power exists, even for Superman, and that it demands great restraint for the superhero. For Batman, Doomsday is a proof that the Justice League Unlimited is too powerful, and that Superman may become a Justice Lords Superman one day, as a result of Lex Luthor's and The Project Cadmus' machinations. Superman reassures his friend.
The Justice Lords form the basis of the Brainiac-Luthor crisis and of the reality that the Justice League Unlimited may prove over-powered. There remains the idea that, due to unlimited power, the Justice League Unlimited may resort to evil, faced with impossible choices and that Superman may become a Justice Lords Superman. According to Amanda Waller's computer simulations, the death of the Flash may be the catalyst for a super-powered war between the US government and the Justice League Unlimited.
Much of the thread of this season, then, is preventing that thread from realizing, and for Superman from going to the side of evil. There always remains the fear that Flash may die and that Superman may become evil, as a result though Lex Luthor dies at the hand of Superman's heat vision. This is a problem of destiny and time eventuality, of a series of choices that lead to an ineluctable end: the fall of Superman and the death of the Flash at the hands of Lex Luthor.
Doomsday presents the fear of absolute power, of a threat that cannot be contained by Batman's strategy, Martian Manhunter's technology, or by Superman's unquestionable might. Doomsday is an eventuality, the eventuality of death and of a Kryptonian clone that has been trained to hate the greatest symbol of America: Superman. In this threat, emerges the reality that America may turn against its greatest symbol in order to oppose totalitarian power and the danger of drugs and human trafficking.
During the Doomsday Sanction, General Eiling sends a Kryptonite missile to San Baquero to kill Doomsday, kill Superman and end drug trafficking. The Cadmus Project does not hide its intentions to completely incapacitate the Justice League Unlimited and deal with Superman in a lethal manner.
The Cadmus Project presents Doomsday as the ultimate test of power for Superman, and presents Doomsday as a killing machine, an unstoppable machine trained to kill Superman. Doomsday seems intent on causing mass destruction, and the fact that he encounters Superman on an evacuation of a volcanic eruption on San Baquero island raises the question of weapons of mass destruction.
General Eiling orders a Kryptonite missile, a weapon of mass destruction to San Baquero addressing the question that nuclear weapons might be used in order to deal with the super power challenge.