|Appeared in||Justice League Unlimited: CADMUS Crisis|
Matters came to a head when the The Question, who had stolen top secret Cadmus files, was captured by Luthor and tortured by Moon for information. Superman and Huntress broke into Cadmus headquarters in New Mexico to rescue him. Captain Atom, bound by his duty to prevent this friendly extraction, attempted to subdue the raiders, but was defeated by Superman and brought to the Watchtower with the Question as well. Afterward, the Justice League debated on their next move in response to Cadmus with the idea of a forceful approach gaining some interest. However, Green Arrow, who was recruited by Batman to be the team's political conscience for precisely this kind of situation, calmed the waters with a sophisticated assessment concerning their apparent enemy's reason for existing: self defense in the event that the Justice League descended into the villainous excesses of the Justice Lords. Although the team accepted the argument, events went immediately out of control with Watchtower's orbital laser cannon suddenly going into its firing sequence apparently on its own. Despite the League's best efforts to stop it, the weapon fired down on the Cadmus facility, destroying it and causing massive devastation in the surrounding area. However, Waller had already evacuated Cadmus' personnel and equipment to another facility, because of the security breach caused by Question's rescue.
Though the Justice League swore to the President that they had not fired the cannon, six of the seven founding members (Superman, Wonder Woman, John Stewart, Shayera Hol, J'onn J'onzz, and the Flash) handed themselves over to government custody as a sign of cooperation. Waller, seeing the strike as clear retaliation for taking The Question, disobeyed the President's order to wait, and ordered Galatea to lead an army of Ultimen in a full-scale attack on the Watchtower. However, the League was able to hold their own against the clones.
In the midst of the attack, however, Batman confronted Waller again and revealed that she had been set up by Luthor, who had access to a lot of Cadmus' technology. Realizing this, Waller ordered Galatea to stand down. It was then shown that Project Cadmus' single operational flaw was revealed: no counter for the countermeasures. The unstable Galatea ignored the order in an effort to murder Supergirl, and she was only stopped due to the efforts of Steel and Supergirl.
While providing funding to Cadmus, Luthor had been interested only in his own agendas: destroying Superman and making himself both superhuman and immortal. He had stolen Cadmus technology allowing him to fire the cannon remotely, and to build a second version of AMAZO to transfer his consciousness into. Had it worked, it would have been a masterstroke: not only would he eliminate his unwitting partners and create a perfect body for himself, he would turn public opinion against the Justice League so as to make killing Superman an act of heroism. Hoping to at least stop Luthor, Waller destroyed his prototype android and released the founding members... only for Brainiac to emerge from within Luthor. Using the Dark Heart stolen from Cadmus, Lex Luthor and Brainiac merged into a single being bent on absorbing the knowledge of the universe, starting with Earth and nearly defeated the Justice League. Fortunately, the Flash managed to stop the Luthor/Brainiac hybrid. It also taught Waller herself that the Justice League still had the peoples' best interests at heart. Cadmus was disbanded, its personnel re-assigned, and its research was classified.