Jack Ryan is sworn in as President of the United States minutes after becoming Vice-President. With most of Congress, the Joint Chiefs of Staff of the U.S. military, much of the senior staff of the Executive Office of the President, the Supreme Court, and all but two members of the Cabinet dead in a terrorist attack committed by a lone Japan Air Lines pilot, Ryan is left to represent the United States virtually all by himself. Ryan deals with various crises, ranging from domestic and foreign policy, to reconstituting the House and Senate, a challenge to his legitimacy by his Vice-Presidential predecessor, scandal-tainted Ed Kealty, and a brewing war in the Middle East. After learning that the majority of the government is dead, two anarchists decide to capitalize on the situation by killing both Ryan and Ed Kealty, using a cement truck filled with an ANFO mixture.
When the President of Iraq, Saddam Hussein, is assassinated by an Iranian member of his own security detail, the leader of Iran Ayatollah Mahmoud Haji Daryaei takes advantage of the power vacuum and launches an unopposed invasion of Iraq, uniting the two countries into one called the United Islamic Republic (UIR).
With assistance from India and the People's Republic of China, the UIR plans to transform itself into a superpower by conquering Saudi Arabia. A series of Iranian-backed terrorist attacks follows, designed to cripple the United States. Terrorist attempt to kidnap Ryan's youngest daughter Katie Ryan but fail due to the intervention of FBI agent Patrick O’Day. Iran then launches a bio-warfare attack using a new Iranian-developed airborne strain of the extremely lethal Ebola virus. Meanwhile, the UIR goes to war against Saudi and Kuwaiti forces and the few uninfected American units are rushed to the region to stand by them. Ryan restricts interstate travel, and closes schools and businesses to prevent the virus from spreading. The bio-war attack fails due to the virus' inability to spread effectively. China also 'accidentally' shoots down a incoming airline which attempts a failed landing at Taipei International Airport during a training exercise. The landing kills many people on-board including American citizens.
Ryan then enacts martial law during this time, which inadvertently prevents the anarchists' assassination attempt because interstate travel has been prohibited. During a routine police check at a truck stop, one of the anarchists panics, drawing police attention to their unusual truck.
In a matter of days, with the combined strength of the Kuwaiti, Saudi Arabian and American armies, they begin to seriously damage the UIR's military resources, soldiers and morale by destroying two entire corps of the UIR's army. Eventually, the triumvirate of the three countries win the war.
At the same time, President Ryan tasks Domingo Chavez and John Clark with a secret mission. They set up a laser guidance device in an apartment facing Daryaei's home, allowing US aircraft to target a precision bomb upon it and bring the house down on the demagogue's head. Simultaneously, during a press conference, President Ryan shows the destruction of Daryaei's residence on live national television and tells the international community that they will only hurt those who are specifically responsible for attacking America. Ryan assassinates Daryaei just after another attempt on Ryan's life by an Iranian sleeper agent in the U.S. Secret Service, is foiled and the assassin is flushed out when he finds the rounds SIG p228 he's carrying have had the propellant from the rounds removed, leaving only the primer. He's then arrested by Secret Service agent Andrea Price, Inspector O'Day and Director Dan Murray from the FBI as he crumples in defeat at the foot of the oval offices desk.
Ryan threatens to bomb bio-warfare targets in Tehran unless the surviving people responsible for the bio-warfare attacks are extradited to America to face charges.
Afterwards, the American people accept their new President, and he decides that he will in fact run for election to a term in his own right.
- The book is so named because President Ryan governs mainly by issuing executive orders, as opposed to working with the Congress to pass legislation or deferring to state and local governments. This is because most of Congress, as well as the Supreme Court and most of the cabinet were killed in the same terrorist action which elevated Jack to the Presidency. In particular, acting on advice of his wife, a physician, in regard to the biological weapon threat, Ryan restricts interstate travel by executive order. In a move designed to embarrass and undermine Ryan's presidency, resigned Vice-President Ed Kealty files a lawsuit alleging Ryan acted unconstitutionally in restricting the travel of US citizens. While ruling in Kealty's favor on constitutional grounds, the lawsuit also ends Kealty's claim to the Presidency, since he inadvertently acknowledges Ryan as President.