As the White House reels from the kidnapping of Zoey, the government is temporarily passed from the distraught Bartlet to Speaker of the House Glenallen Walken. First Lady Abbey Bartlet staunchly supports her husband, but the trauma forces her to confront Bartlet with the notion that the crisis was the direct result of the assassination of a dangerous foreign official he ordered months ago.

The international crisis concerning the terrorist abduction of Bartlet's daughter Zoey reaches a critical point as Speaker of the House Glenallen Walken, the acting President, orders the bombardment of Qumari terrorist camps. The kidnappers issue a 24-hour deadline for the removal of American troops from Qumar.

Following a harrowing chapter in the nation's history, the White House celebrates the Fourth of July. Bartlet endures the painful process of nominating a candidate for vice president. But his first choice will have a difficult time getting approved. Meanwhile, while the reclusive First Lady tends to personal matters, Amy champions Abbey's violence prevention provisions for an upcoming bill.

A renowned North Korean pianist is greeted at the White House for a solo performance, but the formalities change when the musician slips a message to the President stating that he wants to defect. Despite C.J.'s passionate argument, others counsel Bartlet that granting the defection would endanger crucial ongoing negotiations with the nation.

After Josh is hailed as the "101st Senator" in a newspaper profile, he clashes with conservative Senator Carrick, a Democrat from Idaho. Will gets a flattering offer from the newly approved Vice President, Robert Russell, while C.J. runs afoul of Leo's temper.

Bartlet is preoccupied with a killer tornado in Oklahoma and flies there to lend his support. Meanwhile, Leo worries about several crises in the capital that need the president's immediate attention. Josh fears the worst after a political miscalculation costs the Democrats dearly. And Donna becomes concerned about Josh's welfare after he becomes Washington's latest target of scorn.

The President's staff wrangles with new Speaker of the House Jeff Haffley over the pending federal budget. Meanwhile, Toby dispatches former Supreme Court clerk and personal friend Joe Quincy to check on the condition of stricken Chief Justice Roy Ashland, an elderly Supreme Court icon. With the budget deadline quickly approaching, aggressive advisor Angela Blake faces a mighty challenge.

A disastrous fiscal crisis looms when the federal government is shut down after the President and the powerful Republican Speaker of the House disagree over an extra two percent in budget reductions that would trim many of Bartlet's key social programs. Opinion polls reveal that the public blames the Democrats for the impasse. As Leo, Josh and Toby send the staff home, the trio remains uneasy.

The festive Christmas spirit at the annual White House tree-lighting celebration is dimmed when the President learns that Christian relief workers have been jailed in Islamic Northern Sudan. Bartlet welcomes his three independent daughters, Zoey, Liz and Ellie, and is surprised to learn that Liz's husband, Doug Westin, wants to vie for Congress in New Hampshire.

When a former President of the United States dies, the two remaining ex-Presidents fly on Air Force One with Bartlet to attend the funeral. Onboard, Bartlet's two historic guests partake in a lively debate about their administrations. Their past mistakes haunt the current administration including a recent event--protestors have surrounded a Saudi Oil headquarters, taking 200 hostages.

Toby finishes the State of the Union Address a few weeks early, and a pregnant Joey Lucas polls responses to the speech from everyday people. Charlie is intrigued by Meeshell Anders, an aspiring female journalist with a secret. Abbey pressures her husband to pardon a Native American tribal leader convicted of killing two FBI agents in North Dakota. Bartlet pardons over 30 inmates.

Toby convinces Bartlet to secretly sanction his solo attempt to make history by reforming Social Security, but Toby's efforts to recruit a Republican senator and a Democratic cohort are publicly divulged--forcing the administration to back down while Josh and Leo are left clueless and furious. An equally unaware C.J. parries with a reporter who’s ready to print all the backstage details.

When the flash of a secret nuclear detonation is detected over the Indian Ocean, Bartlet calls upon his people to investigate which nation now has the atomic bomb--and since conventional thinking favors Iran, Bartlet orders bombers into the air to destroy that nation's most likely uranium-enriched targets. Meanwhile, Josh chides NASA personnel on the future of space exploration.

When five crew members of an airborne Thunderchief are shot down by North Korean jets near the hostile country, President Bartlet dispatches a Navy SEAL team to retrieve them--prompting Leo to recall his harrowing experience when he was downed over North Vietnam. Meanwhile, C.J. accepts the challenge of dueling on live television with an opinionated, conservative talk show host, Taylor Reid.

The Bartlet administration reels from press leaks that former Vice President Hoynes is preparing a tell-all book that will embarrass the President and Leo as Hoynes plans to become a candidate for President of the United States. The newsflash first stuns C.J. live on the air as she jousts with acerbic pundit Taylor Reid. Josh welcomes the mayor of Washington, D.C., to the White House.

Bartlet becomes furious when a rival conservative congresswoman tries to end funding for a controversial medical study by exposing the fact that Bartlet's daughter Ellie is working at the institute. As Toby searches for the internal White House leak that led to Ellie's press scrutiny, Josh tries to convince an old college friend to remain in contention as a judge on the 6th Circuit Federal Court.

When a Republican Supreme Court justice suddenly dies, the Bartlet administration scrambles to find a worthy replacement, and the halls are filled with candidates. But the President senses that the process is a political minefield until Josh devises a wild plan that could also create an opening for Evelyn Baker Lang, a liberal who would be an unthinkable choice.

Producing a program on past and present White House press secretaries, a television documentary crew follows C.J. around to film a "typical" day. But the presence of outsiders adds stress when a crisis involving a terrorist shootout with the FBI has a smiling C.J. trying to keep the story a secret. Meanwhile, C.J. supervises her team in preparation for a formal papal visit with Bartlet.

On the eve of the President's controversial trade summit meeting in Brussels, Josh is troubled when he learns that Bartlet will reverse his position concerning the loss of American jobs to foreign nations. C.J. is frustrated with a new Federal Communications Commission ruling. Meanwhile, the administration tries to downplay job-loss statistics.

After attending a formal dinner, Bartlet and his staff experience an emergency quarantine inside the West Wing when the environmental hazard monitor detects a dangerous foreign substance. The unexpected lockdown creates odd couplings of people forced to occupy small rooms together. Secret Service agents and hazardous materials inspectors search for the source of the anomaly.

Donna and Admiral Fitzwallace travel with a few Congressmen to the disputed Gaza Strip on a fact-finding mission. But the killing fields soon claim some members of the delegation when a deadly bomb shatters their vehicle, prompting Bartlet to consider targets for military action. In flashbacks, Donna is attracted to a dashing British photojournalist.

In the season finale, after the murders of high-ranking U.S. officials in the explosive Gaza Strip, Bartlet weighs appropriate military action. A wary Josh meets with a mysterious foreign operative while tending to Donna, who is fighting for her life.