Seven hours have passed since Zoey’s kidnapping, and all eyes are on the situation as the world waits for news. After Bartlet evoked the 25th Amendment, Speaker of the House Glenallen Walken, now acting president, reviews military options upon receiving a ransom note from the terrorists. For Zoey’s safe return, the terrorists demand that U.S. troops pull out from Saudi Arabia and Qumar as well as the release of Pakistani terrorists. Meanwhile, the staff worries that Walken will order military action against Qumar; Charlie stays with Bartlet instead of serving acting President Walken; Danny threatens to release a story about the assassination of an official from Qumar; Josh continues to search for Vice Presidential candidates for when Bartlet returns to office; and Toby and Will prepare two speeches -- one if Zoey is alive and one if she isn't.
As the kidnapping crisis heightens, acting President Walken orders the bombing of terrorist training camps in Qumar. The kidnappers issue the U.S. a 24-hour deadline for the removal of American troops from Qumar. Meanwhile, Josh is certain that Walken’s aides are going to use the situation to get their conservative agenda though Congress; and Toby visits his newborn twins all while overseeing the writing of two versions of a presidential speech, each dependent on Zoey’s fate.
In the wake of kidnapping situation, Bartlet makes his return to the Oval Office and turns his attention to finding a new Vice President. But this proves to be a difficult process when Bartlet has a tough time getting his first choice, secretary of state Lew Berryhill, through the approval process. Meanwhile, the First Lady continues to deal with the trauma of the kidnapping, and things are made worse when the Qumari assassination is exposed. Meanwhile, Josh is upset after being confronted by Amy, and Donna deals with Ryan, the new intern.
The White House welcomes a world-renowned North Korean pianist for a performance, but Leo worries that the pianist’s wish to defect will interfere with nuclear disarmament talks. The staff works to get Bartlet’s choice for Vice President, Bob Russell, approved by both the House and the Senate, but one “nay” vote could embarrass everyone. Meanwhile, Will and Toby are humiliated when a draft of a speech is accidentally substituted for the final draft of the speech.
It’s Josh’s birthday, but Will receives a gift instead: an offer to be newly confirmed Vice President Russell’s top aide. C.J. has to deal with Leo’s temper when she doesn’t stick to the administration’s script concerning an EPA report. Amy lands herself in a similar situation when her pushing for funding of the First Lady's agenda on violence prevention evokes the wrath of the President. Meanwhile, Josh is hailed as the "101st Senator" in a newspaper profile, then goes head-to-head with Senator Carrick over the approval of a backlog of military promotions.
Josh lands himself in hot water due to his role in Senator Carrick's switch to the Republican Party. Upon seeing this, C.J. talks to Donna about how to look out for Josh now that he’s not the party’s favorite person. Bartlet is preoccupied after a deadly tornado devastates Oklahoma and flies out to Oklahoma to lend his support to the community, but stays longer than he originally planned. Back in Washington, Leo worries about several crises that need the President’s attention, including the capital-gains tax, the chancellor of Germany and escalating hostilities between Greece and Albania.
While the staff debates Speaker Haffley over the federal budget, Toby enlists the help of Joe Quincy to persuade Chief Justice Roy Ashland to retire after recent health problems. Meanwhile, Josh watches as the rest of the staff negotiates with Congressional Republicans over the budget; and C.J., as well as President Bartlet, worry about Zoey’s television interview with a reporter who’s known for being able to expose raw emotions.
Bartlet and the Speaker of the House continue to disagree about the budget, and the fiscal crisis results in the federal government being shut down. Opinion polls show that Americans blame the Democrats for the halt within the government, damaging the administration’s approval ratings. Josh, Leo, and Toby send the rest of the staff home while Bartlet unfolds a bold plan to challenge the Republicans and get the administration up and running once again. Meanwhile, Abbey emerges from her brief self-imposed hiding for a state dinner that she may have to cook for.
Christmas spirit has once again returned to the White House, and the entire Bartlet family comes together for the annual White House tree-lighting ceremony. But everyone’s spirits soon fall when Bartlet learns that Christian relief workers have been imprisoned in Islamic northern Sudan. Later, Bartlet is surprised when his son-in-law informs him of his Congressional ambitions. Elsewhere, Toby tries to keep the administration out of a controversial debate when the licenses of some Oregon are suspended after they order drugs in an assisted suicide.
Bartlet joins “former president” Glenallen Walken aboard Air Force One to fly to the services for another former president who recently passed away. While at the funeral, Bartlet continues to monitor a building situation in Saudi Arabia as freedom protesters threaten civil war. Back in Washington, Josh mediates between two representatives over a copy of the Bill of Rights, while C.J. meets with a Pentagon scientist about invasive security innovations. Elsewhere, Leo learns that his ex-wife is engaged to be married.
With the State of the Union address nearing, Bartlet goes over a long list of prisoners that qualify for pardons while considering the potential political repercussions due to "the benign prerogative". Charlie meets an attractive woman and shares small, private White House facts, and is horrified to learn that she’s a White House reporter. Meanwhile, Toby and Joey Lucas "mall test" an upcoming presidential speech; Abbey vows to be more pro-active when it comes to influencing Jed; and Bartlet entertains a couple from Colorado.
Toby convinces President Bartlet to sanction a secret mission to “save” Social Security, but the administration is forced to retreat when efforts to recruit a Republican Senator are leaked. Meanwhile, C.J. deals with a reporter who threatens to write a story about the efforts; and the female staffers complain to Josh about the newest employee.
A nuclear bomb explodes in the Indian Ocean, but no one in Washington knows who set it off. Bartlet and the staff scramble to figure out which country has nuclear capabilities, and when their thinking leads them to believe it's Iran, Bartlet orders bombers to destroy Iran's uranium-enriched targets. Meanwhile, Josh yells at NASA about the future of their program until he goes stargazing with a female administrator. Elsewhere, C.J. is fuming after being labeled "Chicken of the Week" by a local news station; and Will lobbies for a new "policy focus" for Vice President Russell.
A Navy fighter pilot collides with a North Korean jet and the crew goes missing in hostile North Korean territory. Upon hearing this, Bartlet orders an elite Navy SEAL team on a rescue mission, triggering Leo's memories of being downed as a pilot over North Vietnam. Meanwhile, C.J. decides to go head-to-head on air with the newscaster who labeled her "chicken of the week"; Josh is angry after being undercut by Ryan in a briefing with the President; and Bartlet poses for his official portrait.
The staff is shocked when John Hoynes is back in the news via a magazine article about how Hoynes is claiming that Bartlet and Leo tried to talk him out of resigning, as well as how he is writing a tell-all book that will embarrass the Bartlet administration. C.J. learns the news from cable talker Taylor Reid, while on Reid's live show, leading to disastrous results. Meanwhile, Toby fights with Union representatives over Chinese trade policy; Josh and Ryan go over military base closures; and D.C. mayor decides that school vouchers would be best for the city.
Bartlet becomes enraged when a Congresswoman uses her knowledge that Ellie Bartlet is working at a scientist for the National Institute of Health in order to get funding for a controversial medical study. Toby scrambles to find the internal leak who exposed Ellie's position while Josh meets with an old friend who happens to be a judicial nominee that's being held up in committee. Meanwhile, Abbey appears on an episode of Sesame Street, despite C.J.'s political concerns, with Elmo and Big Bird as a doctor who gives Elmo a check up.
When a Supreme Court justice dies suddenly, Bartlet and his staff rush to find a nominee to replace the late Republican justice. As the staff go over hundreds of possible candidates, Bartlet begins to think the nominee will be a "political minefield" until Josh comes up with a plan to get a liberal, Evelyn Baker Lang, approved by the Senate. Potential nominees are invited to the White House -- mainly to mislead the press -- but suspicions are heightened when Bartlet meets with a young, controversial judge.
A documentary crew comes to the White House to film a documentary about a day-in-the-life -- their main focus being C.J. However, the constant presence of the crew adds stress to an already stressful FBI-standoff crisis in Washington State that C.J. is trying to keep under-wraps for the time being. During the day, Meanwhile, C.J. and her staff also prepare for Bartlet's upcoming trip to the Vatican to visit the Pope.
The night before Bartlet's trip to Brussels to sign a trade pact, Josh is torn knowing that the pact will reverse Bartlet's stance on outsourcing American jobs to foreign countries. C.J. becomes increasingly frustrated over the FCC's ruling concerning companies increasing ownership of television stations. Meanwhile, Donna confronts Josh about her limited role on his staff; and Kate Harper, the new Deputy National Security Adviser, meets with Bartlet for the first time.
After a fancy dinner at the White House, President Bartlet and his staff are placed on lock-down when a suspicious substance is detected. While waiting for clearance to leave, the staff are forced to stay in small rooms where they reflect on their past and their relationships with one another. However, the night turns confrontational when Toby accuses Will of being a backstabber to the President. Meanwhile, Debbie and Charlie agree to be inspected; C.J. gives Donna advice; and Josh tries find out why his joke was omitted from a speech.
While on a fact-finding tour in the Gaza Strip, Donna is seriously injured in a terrorist car bombing that leaves three other Americans dead. The staff, as well as the President, find it hard to deal with their emotions while trying to come up with an official response to the attack. In flashbacks, Donna recalls falling for a British photojournalist who photographs deadly and bloody violence.
With Donna recovering in a military hospital in Germany, Bartlet struggles to decide what "appropriate" military action to take against the Palestinians. Fears are heightened when Israel launches its own strikes and the President is unable to contact the chairman. Josh, in Germany to see Donna, comes in contact with a mysterious foreign operative. Meanwhile, Bartlet, in a bullet-proof vest and with extra Secret Service protection, throws the ceremonial first pitch of the Major League Baseball season.