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 (avenging the death of his son and brother in Debt of Honor), Ryan is left to represent the United States virtually all by himself. This novel follows Ryan as he 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 (at the time of publication, the book referred to then-President Saddam Hussein although he is only mentioned once by name. However, he is based on Saddam, and has many similarities including choice of sidearm) 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. Following a series of Iranian-backed terrorist attacks designed to cripple the United States, including a failed kidnap attempt on Ryan's youngest daughter in which all except two of her secret service detail is taken out (despite killing 5 of the 7 terrorists) and she's only saved by the intervention of FBI agent Patrick O'Day who double taps the remaing terrorists with his 10mm S&W 1076. And a bio-warfare attack using a new Iranian-developed airborne strain of the extremely lethal Ebola virus, 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 reduce the virus spreading. The bio-war attack fails for a reason well known to virologists: Ebola outbreaks quickly exterminate a small group of people, then burn out because they run out of new hosts; other viruses that kill less efficiently manage to spread to larger communities. Iran's ally 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.
He also orders the country into 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 calls Ding Chavez and John Clark into 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 (similar to the previous assassination of the President of Iraq), 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.
After-wards, 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.