The War-Kohn have invaded the Earth. As a prelude to their invasion, a mutagenic compound was dispersed, across the globe, transforming a third of the populace into War-Kohn soldiers. After an attack on the Justice League of America's satellite headquarters, the War-Kohn target Earth's nuclear defenses. At a nuclear missile base in Nevada, the Batman, and the Flash, engage the War-Kohn. At a nuclear missile base in Siberia, the Phantom Stranger, and Wonder Woman engage the War-Kohn. In the South Pacific, Aquaman attempts to keep the War-Kohn from taking possession of a nuclear submarine.
The War-Kohn commander, Karvas-Kun, dreams of his coming victory, and enslaving the populace of Earth. Aboard the Justice League of America's satellite headquarters, the Elongated Man, and the Red Tornado, stand helplessly by, watching their teammates fight a losing battle against the War-Kohn. Aquaman's attack on the War-Kohn reveals a possible weakness to the Elongated Man. On the home world of the Treasurers, the Justice League of America fight a desperate battle against the War-Kohn, while the Atom tries to breach a prison vault.
The Atom succeeds, but though he encounters a number of War-Kohn prisoners, George Arthur Stuart is not among them. The Atom releases the prisoners, who join the Justice League of America, in the the fight against the War-Kohn. Fearing the Justice League of America's impending victory, the Treasurers spirit Stuart away, off world. The Justice League of America pursue the Treasurers' ship. The Elongated Man, and the Red Tornado, join Aquaman, in the South Pacific.The Elongated Man has sussed out the War-Kohn's technological weakness to water.
Aquaman telepathically summons a host of marine life, creating a tidal surge that shorts out the War-Kohn's weapons. A physicist, Dave Dorman fights his way through the streets of Stockholm, in search of his fiancee, the Pop star, Olivia St. James. The Justice League of America follow the Treasurer's vessel to the home world of the War-Kohn. The Justice League of America subdue the War-Kohn, and recover Stuart. On Earth, the Justice League of America fight the War-Kohn to a standstill. The Green Lantern teleports Superman to Nevada, the Black Canary and the Green Arrow to Siberia, and himself to the South Pacific.
Fully assembled,on Earth, once more, the Justice League of America defeat the War-Kohn. The Justice League of America attack Karvas-Kan, ending the conflict. The Atom places Stuart in a genetic transmuter device, and uses Stuart's DNA to restore the humans transformed into War-Kohn. Stuart, it turns out, contains the genetic template for all of humanity, stored in his own DNA. Dorman is finally reunited with James. Though the crisis has passed, the Atom points out that the reason Earth was vulnerable to the Treasurers still exists, and that their problems might not be completely solved.