Putin's Virus begins with a brilliant student--a loner unloved and discriminated against in the physics department of a university. He discovers a way of fusing together nuclear material without the use of high explosives. His technique for doing it is used to make suitcase-sized bombs, which are used by the US military to be planted in every major city of the USSR. But an agent is caught, the suitcase bomb analyzed, and the knowledge of its construction is used by Russian agents. These agents are labeled as "viruses" with the prefix Putin in homage to the deceased Russian leader. These Putin Viruses infiltrate the US via the town of Nogales using supremely efficient Mexican smugglers who know how to circumvent any wall, fence, border guard, or barbed wire.

In one American city, a Russian agent has a heart attack, dies, and his effects are found to contain code. The FBI is informed, and an agent who has no chance of advancement is sent to investigate. From his findings, and with a girlfriend helper, he realized that atomic bombs are already readied in several American cities. Piece by piece, he brings together the plot to set off atomic bombs in every major American city. However, one Russian agent is elusive, and upon his command, the other viruses will set off their atomic bombs to detonate via timers to give them time to leave the area by plane or submarine.

The FBI agent and his girlfriend track this Russian agent down to Sugarloaf Mountain just outside of Washington DC. There, atop the mountain, the agent plans to detonate an atomic bomb whose power is ten times the power of the Hiroshima bomb. It is a fight to the death to stop him and, therefore, the other viruses!