In New York City, Japanese industrialist Raizo Yamata purchases a controlling interest in an American mutual fund group. He flies to Saipan and visits Banzai Cliff— the site of his parents' suicide during the American invasion of the island at the close of World War II — to buy a large tract of land.
Meanwhile, in eastern Tennessee, a car accident involving two Japanese-made vehicles leads to the deaths of six people. Revelations about manufacturing and shipping errors that led to the deaths stir long-standing resentment against Japan's protectionist trade policies. As trade negotiations between the United States and Japan grind to a halt, Congress passes a law enabling the U.S. to mirror the trade practices of the countries from which it imports goods. The bill is immediately used to reciprocate Japan's non-tariff barriers, cutting off the U.S. export markets upon which the Japanese economy depends.
Facing an economic crisis, Japan's ruling corporate cabal, led by Yamata, decides to take military action against the U.S. Along with covert support from China and India, they plot to curtail the American presence in the Pacific and re-establish the Greater East Asia Co-Prosperity Sphere. In the wake of these developments, Jack Ryan is recruited as National Security Advisor by President Roger Durling. Meanwhile, CIA officers John Clark and Domingo Chavez are sent to Japan to reactivate a former KGB commercial spy network (codename THISTLE ) in order to gain intelligence.
Meanwhile, Japan has covertly developed nuclear weapons and with SS-18 designs bought from USSR has fabricated and deployed several ICBMs.
Japan launches the first phase of its assault, sending Self-Defense Force units to occupy the Mariana Islands, specifically Saipan and Guam. The invasion, with the troops transported by commercial airliners, is virtually bloodless. Meanwhile, during a joint military exercise, Japanese ships "accidentally" launch torpedoes at the U.S. Pacific Fleet, destroying two submarines and crippling two aircraft carriers, the Enterprise and the John C. Stennis . As a result, the U.S. capability to project power into the western Pacific is drastically reduced.
An immediate retaliation is forestalled by the second phase of the Japanese offensive: an economic attack. Even as the military offensive begins, Japan engineers the collapse of the U.S. stock market by hiring a programmer who is a consultant for an exchange firm to insert a logic bomb into the system, which when triggered blocks the storage of all trade records made after noon on Friday. The Japanese also assassinate the chairman of the Federal Reserve. With a massive economic crisis and subsequent mass panic, the Japanese hope that America will be too distracted to quickly respond to Japan's military actions.
Japan immediately sues for peace, offering international talks and seemingly free elections in the Marianas to delay a U.S. response. Negotiators secretly reveal to the U.S. that Japan has obtained nuclear ballistic missile capability. The Japanese oligarchs, led by Yamata, believe that offers of negotiation and the nuclear deterrent, defended by a seemingly impregnable AWACS system; modified Boeing E-767 Kami , will cause the U.S. to concede Japan's advantage. With two of America's twelve carriers disabled, and the rest pinned down by a mix of maintenance and international crises elsewhere, Ryan has few resources with which to defend American interests.
Despite his typical focus on military issues, Ryan advises President Durling to deal with the economic crisis first. Ryan also realizes that Japan's deletion of trade records could be an advantage in responding to the economic threat. He engineers a "do-over", where all of the transactions that were deleted on the day of the mass deletion are ignored and all trade information is restored to its condition at noon of that day. Accompanied by a presidential address to the nation and behind-the-scenes bullying of investment banks, the plan is a success: America's stock market is restored with only minor disruption. Concurrently, a group of American investment banks start a massive economic unloading of Japanese investment products, effectively eliminating any gains made by the Zaibatsu.
The United States eliminates Japan's AWACS system through a series of "accidents" and low-profile military attacks using widely dispersed U.S. assets, allowing B-2 bombers to destroy the ICBM silos.
In one staged accident, Clark and Chavez blind two incoming Japanese AWACS pilots with a high-intensity light and cause them to crash on landing. A fictitious technical warning of a problem with the automatic landing system was used to create the impression that the attack was an accident. They then managed to rescue Japan's moderate former prime minister Koga from his house arrest so that he could be used in later peace talks.
The Air Force uses an attack by stealthy F-22 fighters to further damage Japan's air defenses.
An Army special operations team is airdropped into Japan to support covertly inserted Comanche helicopters. One helicopter is used to attack another AWACS plane with air-to-air missiles while several others use Hellfire missiles to kill members of Yamata's cabal.
Meanwhile, Admiral Robby Jackson liberates the Marianas with little bloodshed by using a combination of cruise missiles and carrier air attacks to severely damage the Japanese aircraft stationed on the islands which forces the Japanese commander to surrender his troops. The damaged John C. Stennis been stealthily removed from Pearl Harbor while it was supposedly under repair for damage to the propellers. However, the damaged carrier had two workable shafts which gave it enough speed for air operations so it was pressed into emergency service for the attack.
Outmaneuvered and cornered by the United States military and economic response, Japan's aggressive prime minister Hiroshi Goto resigns, ceding power to his rescued predecessor Koga. Yamata is arrested, and the new Japanese government accepts America's generous offer of status quo ante .
Throughout the book, President Durling faces another, less important political crisis: Vice-President Ed Kealty is forced to resign after being accused of drugging and raping a former member of his staff. With the crisis over, President Durling nominates Ryan as vice-president for his services during the crisis. However, an embittered Japan Air Lines pilot—driven mad by the deaths of his son and brother during the conflict—flies his Boeing 747 directly into the U.S. Capitol during a special joint session of Congress.
The president, as well as nearly the entire Congress, the Supreme Court, and many other members of the Federal Government are killed in the attack. Ryan, who had been confirmed as vice-president moments before, is exiting the Capitol Building through a tunnel and narrowly escapes the explosion. He first realizes that he is suddenly the new President of the United States when his Secret Service agent Andrea Price addresses him as "Mr President." He takes the oath of office and begins an uncertain term as President.