Duncan's daughter Lilly, who is studying in Paris, receives a coded message from a young Eastern European woman named Nina.

He arrives at a safe house, where he learns that Nina and Augie created and distributed a highly destructive computer virus called "Dark Ages" for Cindoruk, but they warned the US when they realized what it would do.

In a meeting with the Prime Minister of Israel, Prime Minister of Russia, and the Chancellor of Germany, Augie explains the full extent of Dark Ages: it is an attack that would completely destroy the data on every internet-connected device in the US, leaving the country vulnerable to outside attack and forcing the government to retreat from its foreign policy objectives.

Duncan reveals that the US military has quickly built a rudimentary international network to maintain defensive abilities in the event of the Dark Ages virus launching.

At the same time, the Sons of Jihad attempt to kill Augie, but are stopped by the Secret Service and a Marine Corps helicopter.

Duncan learns that Suliman had been sponsored by Russia and a faction in the House of Saud, both of whom wanted to weaken the superpower status of the US so they could expand their territory without interference.

[7] In his review of the novel for The New Yorker, Anthony Lane argues that The President Is Missing "maximizes its potency and fulfills its mission" while commenting negatively on the book's prose, the absurdity of its plot, and the use of product placement.

[12] Nielsen Bookscan, which represents around 85 percent of print book sales,[12] reported that at least 152,000 of the copies sold in its first week were hardcover.

[15] By July 6, 2018, Publishers Weekly stated that the book sold nearly 384,000 copies by the end of June and was the top selling new novel for the entire first half of 2018.