The world watches the desperate search for Zoey Bartlet while rival administrations form an uneasy alliance as a result of President Jed Bartlet invoking the 25th Amendment, causing Speaker of the House Glen Allen Walken, a Republican, to become acting President. The staffs of both men, now forced to work together in the West Wing, weigh options that include a preemptive military strike at terrorist targets — a move that could doom Zoey. Toby and Will prepare two speeches, one for each possible outcome of Zoey's abduction. Also, the full story behind the assassination of Abdul Shareef is revealed, and a deadly terrorist attack occurs in Turkey.

The international crisis concerning the abduction of President Bartlet's daughter Zoey reaches a critical point as acting President Walken orders the bombardment of Qumari terrorist camps and fences with Leo over the impact of his actions. The kidnappers issue a 24-hour deadline for the removal of American troops from Qumar, but an intelligence break brings an end to the crisis. Meanwhile, Josh fumes over his perceived notion that the Republicans will exploit and push forward their own legislative agenda, and Toby visits his newborn twins while pondering what will happen.

Following a harrowing chapter in the nation's history, the White House celebrates the Fourth of July, but most of the staff is not in a cheerful mood. C.J. is moved by the resignation letter of a senior State Department diplomat who could not stomach the Shareef assassination. Bartlet endures the painful process of nominating a candidate for Vice President. His first choice, Secretary of State Lewis Berryhill, cannot be approved and he and his staff are unimpressed with the compromise candidate they end up with, reflecting on how recent events have emboldened the Republicans. Meanwhile, the reclusive First Lady tends to personal matters and expresses anger towards her husband and Leo, Amy champions Abbey's violence prevention provisions for an upcoming bill, the President drops in on a citizenship swearing-in ceremony, and Donna is appalled by a cocky new intern, Ryan (Jesse Bradford).

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 President Bartlet that granting the defection would endanger crucial ongoing nuclear negotiations with Pyongyang. Also, members of the staff work hard to get the President's new choice for Vice President, Colorado Congressman Robert Russell, also known as "Bingo Bob", approved by both houses of Congress and must convince a Democrat who is not a fan of Russell's. Toby and Will express their contempt for the new VP by writing a mock speech highlighting his shortcomings, which is then inadvertently shown on the President's teleprompter instead of their actual speech. Russell is amused by the speech despite its criticism of him, and asks for a copy.

As the Bartlet clan, including a late Ellie, gathers for the White House Christmas tree lighting ceremony, Christian missionaries are arrested in Sudan for proselytizing. Meanwhile, the Drug Enforcement Administration has suspended the license of a doctor who assisted with the suicide of a terminally ill patient in Oregon, where it is legal, the President's attorney general is siding with the DEA; and President Bartlet's son-in-law, Doug Westin, has decided to run for Congress, even though he will not receive the support of the White House.

When former President Owen Lassiter dies, the two living former Presidents, liberal Democrat D. Wire Newman and conservative Republican Glen Allen Walken, fly on Air Force One with President Bartlet to attend the funeral. Onboard, President Bartlet's two guests partake in a lively debate about their administrations. Lassiter and Newman's past actions haunt the current administration when massive pro-democracy protests are held across Saudi Arabia and the protesters surround a compound containing fifty Americans, leaving President Bartlet to decide whether to support the Saudi regime or to risk the fragile status quo by supporting the protesters' efforts. C.J. meets with an eccentric representative from the Defense Advanced Research Projects Agency and Josh and Angela spar over a states' dispute. Guest starring James Cromwell as President Newman and John Goodman as President Walken.

Toby finishes the State of the Union address a few weeks early, and Joey Lucas, who is now pregnant, polls responses to the speech from the public. Charlie is intrigued by Meeshell Anders (Gabrielle Union), an aspiring journalist who does not initially reveal that she will soon become part of the White House Press Corps. Abbey pressures her husband to pardon a Native American tribal leader convicted of killing two FBI agents in North Dakota. President Bartlet opposes mandatory minimums and guidelines for prison sentences and later pardons over thirty inmates who were harshly sentenced under mandatory minimum laws. Toby hires a new assistant, Rina.

Two US aircrew are stranded in North Korea, prompting a difficult rescue operation, and bring back memories for Leo of when he was rescued in Vietnam. Meanwhile, the man who rescued him, now the head of a major contractor for the Department of Defense, faces questions in a Senate probe, forcing Leo into a potentially dangerous conflict-of-interest. Josh is corrected by an intern when he misquotes data in a briefing to the President. C.J. appears on the Taylor Reid show to face his on-air taunts.

When a Republican congresswoman starts a campaign against publicly funded research into sexually transmitted diseases, effectively targeting the President's daughter's work, links emerge to the Vice President's office. The First Lady, reeling from the reaction to her assistance at a health clinic, agrees to soften her image by appearing with characters from Sesame Street. Josh tries to sort-out a deadlock on judicial appointments.

Resentments fester when the White House is locked down after a suspicious substance is found in the air near the Oval Office. Staffers must remain where they are. This is particularly bad news for Toby and Will, whose enmity is increasing in the wake of a Russell speech written by Will that Toby feels undercut the President. Meanwhile, C.J. has some career advice for Donna; Leo and Abbey spar over health issues, personal and political; and Josh gets to know new NSC staffer Kate Harper.