The alien shapeshifters called the Chitauri were defeated by the Ultimates in a decisive battle, but suspicious activity leads the Ultimates to believe that not all of the aliens were destroyed in that cataclysmic attack. Stark Industries has developed a means of quickly and easily detecting Chitauri DNA, but the federal government refuses to adopt the technology, claiming that if the tech is widely available, the Chitauri will find a way to fool it.
Frustrated by the government's seeming unwillingness to protect its own people, Captain America takes matters into his own hands, leaking the technology so that it can be manufactured and distributed throughout the country. His radical actions sow discord among the Ultimates and within the highest levels of government, raising a troubling question: Could this disunity and chaos be playing right into the Chitauri's hands?
Meanwhile, Hank Pym, who desperately wants back on the Ultimates team, has been feverishly experimenting with his ants in the hopes of finding his own alternate method of detecting the Chitauri. When he appears to be successful, it could spell doom for the alien menace -- but only if the Ultimates can finally set aside their differences long enough to recognize their true enemy....