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The senior staff is called back to the White House as "POTUS" (President of the United States) Jed Bartlet is injured, having ridden his bicycle into a tree. Josh Lyman, the Deputy Chief of Staff, is in trouble after a television appearance in which he makes an insulting comment to a representative of a political-connected Christian group; and Sam Seaborn, the Deputy Director of Communications, spends a night with a woman who turns out to be a prostitute. Another subplot is 1,200 Cuban boat refugees, 137 of whom arrive in Miami and request asylum, while 350 are missing in a storm and presumed dead. Bartlet speaks bluntly to the Christian group Lambs of God.

Sam jeopardizes his political future when he decides to pursue a relationship with the prostitute whom he met recently. C.J. arbitrates a disagreement between the President and the Vice President. Mandy is hired as the West Wing’s political consultant, despite Josh’s objections. President Bartlet connects with his new physician, Captain Morris Tolliver, MC, USN, whose first child was born ten days prior. The episode ends when Leo informs the President that Tolliver died while en route to a teaching hospital in Jordan when Syrian forces shot down his military aircraft on the orders of the Syrian Defense Ministry, killing all on board.

The White House has surprisingly lost five votes for an incremental gun control bill, so the West Wing staff work during the three remaining days to regain the votes for the passage of the bill. After Leo forgets his wedding anniversary, his wife announces that she is leaving him. Josh and Toby encounter difficulties over their personal financial disclosures which are being shared publicly. The last gun bill vote is secured thanks to the Vice President who counted on being the hero of the process.

The staff members participate in Leo's "Big Block of Cheese" Day, when they meet with fringe special interest groups who normally cannot get attention from the White House. Josh receives a card from the National Security Council and later learns that he is the only senior staff member other than Leo who will receive protection in the event of a nuclear attack. Uncomfortable about his special treatment, he eventually returns the card, believing that he does not deserve to be singled out among his friends. Sam and C.J. discuss the possibility of a virus infection going rampant in the U.S., and how it could be contained without available anti-virus. Zoey Bartlet, the youngest First Daughter, arrives at the White House, and the President holds a celebratory chili supper in her honor for the members of his inner circle.

The President and his senior staff deal with major problems – a hostage standoff between the FBI and a group of survivalists in Idaho, a pre-season hurricane headed toward the Atlantic Coast, and the threat of a crippling nationwide trucking strike by the Teamsters – all while preparing for a state dinner to honor the new President of Indonesia, whose behavior is distant and uncommunicative. Toby requests a favor from a senior aide to the Indonesian president; the aide not only refuses but also lectures Toby about human rights, and for being a hypocrite. At the state dinner, the First Lady, Abigail Bartlet, makes her first appearance, and Sam sees Laurie, who is working as an escort for one of the attendees. In a predictable move to evade the storm, an aircraft carrier task group of the US Navy, including two cruisers and two destroyers, gets underway from Norfolk, Virginia, and heads into the Atlantic Ocean; however, the hurricane makes a surprise course change and moves directly toward and across the naval vessels. With difficulty, the President chats via radio with a young petty officer in the radio shack aboard a small ship in the task group.

While the senior staffers discuss the preparations for the Christmas celebration at the West Wing, Toby receives a telephone call from the office of the local coroner, and he responds by meeting a detective of the Metro PD at the Korean War Veterans Memorial on the National Mall to identify a body who had been found wearing a jacket that had Toby's business card in the pocket. Toby becomes emotionally and actively involved with the death of the man, who he discovers was a homeless veteran had served as a lance corporal in the US Marine Corps in the Korean War, and works to find out the man's identity and next of kin. C.J. tries to push for hate crime legislation after a deadly assault on a young gay man but receives little support amongst senior staff. Danny and C.J. continue to discuss the pros and cons of a first date. Sam and Josh, against Leo's wishes, visit Laurie to try and get dirt on Lillienfield and his allies, but she refuses to tell them anything and reminds them to behave as the good guys. Toby and Mrs. Landingham accompany the veteran's brother to his burial at Arlington National Cemetery with an honor guard.

After rehearsing for the State of the Union address, President Bartlet collapses in the Oval Office. An admiral and medical officer from Bethesda diagnoses it as the flu, but the First Lady, Dr. Abbey Bartlet, cancels her trip and returns to the White House to treat her husband. Skirmishes continue along the cease-fire line in Kashmir; Pakistan gives control of nuclear weapons to their field commanders. Leo faces the news media about his alcohol and Valium addiction and recovery, then faces the First Lady about the President's health; Abbey eventually admits that the President has relapsing-remitting multiple sclerosis (MS), and that a fever could be fatal. Josh and Toby continue to wrestle with the speech; C.J. watches Mallory kiss Sam, and has Danny come to her office. Lord Marbury advises the President on benevolent diplomacy, who sends India a message, which produces good results.

The President and staff deal with a study on sex education in public schools refuting the use of abstinence-only techniques, a forthcoming signing of a hate-crime bill, the parents of a young man killed with religious-motivated homophobic violence, and an advance man to the Vice President who has abused his position. C.J. and Danny continue to deal with their relationship. An influential man offers Leo some unwelcome advice, which he refuses. A senior member of the House of Representatives summons Josh and Sam and leans hard on them; they make a deal, which avoids a hearing on Leo and the related inquiries. Sam finds out how Lillienfield and Claypool obtained the information about Leo's addiction and treatment. Leo and a young lady (Liza Weil) agree to give each other a second chance.

Late on a Friday, the Supreme Court declines to set aside the death sentence of a federal prisoner for two drug-related murders and orders the execution to take place early on the following Monday at the Federal Penitentiary at Terre Haute, Indiana. One of the appellant's public defenders is Sam's former bully from high school, who places a last-effort call to Sam in hopes of saving his client through presidential intervention. Sam answers as he unsuccessfully tries to leave the White House for a weekend of sailing, and the two then meet in person. On Saturday morning, President Bartlet returns from Stockholm; Donna finds Josh asleep and hungover in his office after a bachelor party. Sam calls Toby at his temple, while his rabbi presents a sermon against capital punishment, as Sam's classmate found the rabbi and arranged for him to preach to Toby. Meanwhile, Josephine “Joey” Lucas (Marlee Matlin), the deaf campaign manager for a Democratic House candidate from Southern California, using American Sign Language through her interpreter Kenny, aggressively asks Josh why the White House has caused the Democratic National Committee to reduce the funding for her campaign, and then demands to meet the President. When Josh assures her that there is no way for her to meet the President, he appears at Josh's door and gives Joey a tour of the Oval Office. The President calls the Pope and sends for the parish priest (Karl Malden, in his final acting role) whom he knew as a boy; he also discusses the death penalty separately with Charlie and with Joey, who is a Quaker. As Joey and Kenny leave their hotel to return to California, Josh, at the request of the President, offers Joey an apology and a suggestion. The President continues to agonize over his decision and makes a confession to the priest.

Josh is interviewed before a group of college students at Georgetown about a supposedly typical day at the White House. Josh's remarks, including a candid description of his own mistakes, showcases a difficult and challenging day when C.J. has urgent dental surgery and Josh conducts the press briefing in her place with disastrous results, while Sam learns that Judge Mendoza—the nominee to become the next associate justice of the Supreme Court—has been arrested in Connecticut on charges of drunk driving, resisting arrest, and disorderly conduct. Sam, having vetted Mendoza, knows the judge cannot consume alcohol because of a liver condition, and heads to Connecticut with Toby. The two get lost along the way in a rental car, but eventually arrive at the small-town police station, where they work out the delicate situation.

At 3 a.m. aboard Air Force One, President Bartlet, Josh, Toby, C.J., Donna, Zoey, Charlie, and others leave Andrews AFB for a grueling 24-hour trip to Los Angeles. The President expresses concern about a pending 50-50 vote on a Senate bill about a tax credit for the production of ethanol as a fuel, and meets Gina Toscano (Jorja Fox), the Secret Service agent assigned to Zoey. The agenda, filling the day and evening, includes a debate on a proposed amendment to the Constitution to prohibit burning the national flag, a town-hall meeting on school vouchers, and a celebrity-packed fundraising dinner at the home of Ted Marcus (Bob Balaban), the president of a film studio. Ted learns that a conservative congressman has introduced a bill in the House to ban gays from the armed forces and that the White House does not actively oppose the bill, so Marcus threatens to cancel the fundraising event. Josh arranges ten minutes for Marcus and the President alone, and the party proceeds. Joey Lucas attends and explains some interesting numbers to Josh, Sam, Toby, and C.J. Leo, back in Washington, asks the Vice President to break the tie in the Senate in favor of the bill, but the Vice President prefers not to do so because of personal, political, and ideological reasons; however, Sam and Leo arrange for three reluctant senators to vote "nay", thus letting the Vice President off the hook.

The First Lady appears on television on behalf of the Children's Crusade to raise awareness about child slavery, but her efforts are soon overshadowed when the Chairman of the Federal Reserve Board of Governors dies. Leo, to settle the uncertainty in the investment markets, urges the President to announce a successor, but the President decides takes time to make sure, although, according to a leak, the First Lady has expressed her preference, who also happens to be a former boyfriend. Josh and Toby court additional votes in the Congress to run up the score on the vote on a global trade agreement, and a congresswoman gives Sam a courtesy advance notice of a forthcoming announcement about her rider on the exploitation of child labor, which Sam expects to "blow the vote out of the water". Sam speaks with the First Lady, who negotiates for the withdrawal of the rider. The First Lady reveals who leaked her preference and the Bartlets have what they call their first Oval Office fight, but they quickly make up. The White House has received death threats and other hate mail from white supremacists about the relationship between Zoey and Charlie, who argue about their plans for Friday night; later, Charlie shows up at Zoey's dorm room with flowers, other gifts, and an apology.

When the weather suddenly changes just before a speech by President Bartlet, Sam forgets to change the introductory remarks, thus creating a humorous and embarrassing moment. Two members of the Federal Election Commission have resigned, so the staff members start preparing for new appointments; Josh meets with the Senate leadership from both parties, but the conversation does not go well. Both the staff and the press hear a rumor about the circulation of an unknown memo; Mandy volunteers to C.J. that she wrote the memo when she worked for Sen. Russell, and that it outlines both the weaknesses of the Bartlet administration and a strategy to defeat President Bartlet for the nomination for reelection. C.J. demands a copy immediately and Mandy complies. After reading it, C.J. approaches Toby, who shares it with Josh, who comments that their second year has not gone better than their first. Sam and Toby meet with a group of military officers about a recommendation to the President on the service of gays in the armed forces, but that discussion too does not go well; Admiral Fitzwallace, the Chairman of the Joint Chiefs, pops in and offers his advice; eventually the meeting ends without achieving anything. Mrs. Landingham encourages the President to improve his eating choices. C.J. learns which reporter has the damaging memo, and she hears that a story will appear in print the next morning. Margaret has computer and email problems, and Leo reads the memo. The President reads it, then he and Leo have a heart-to-heart chat, after which Leo tells the senior staffers that they will start raising the level of public debate in the nation and let that be their legacy even if they do lose some political battles; they agree that they serve at the pleasure of the President, and Leo tells them to get into the game.

After last-minute quibbling over the wording of several questions, the senior staff start a nationwide telephone poll to measure the job-approval rating of the administration. The majority of the staff think the poll will show a decrease in the rating, but C.J. believes the numbers will go up; however, when the President asks Leo what the senior staff thinks the results will be, Leo omits C.J.'s prediction, which hurts her when she finds out and leads her to speak up for herself and her opinions. Leo gives a snow job to the lone reform-minded member of the Federal Election Commission. With regret, Sam explains to Laurie that he cannot attend her graduation from law school. He later goes against Leo's orders and presents her a gift outside her friend's apartment that night, but someone takes a photograph of the encounter, which was a set-up organized by Laurie's friend, and it reaches the attention of President Bartlet. The President accepts a round-robin plan to change several US ambassadors due to the personal misconduct of the present ambassador to Bulgaria. C.J. spars with the press corps about treatment, rehabilitation, and mandatory minimum sentences for convicted drug users. The President makes a deal seeking reform on soft-money political contributions. Eventually C.J. receives the results of the poll, goes to the Oval Office, and presents them to the President.

Iraqi ground forces, using a surface-to-air missile, shoot down an F-117 Nighthawk of the US Air Force during a routine three-hour patrol of a no-fly zone; the pilot, a 26-year-old captain, survives, but Iraqis are only 10 miles away. President Bartlet orders a military rescue immediately. The staff learns that the Space Shuttle Columbia has incurred a mechanical problem and a resulting delay in its landing, and that Toby's brother is a payload specialist aboard the flight. Later, the officials learn that the rescue of the downed pilot has succeeded. The President, Zoey, and the senior staff go to a museum in Rosslyn, in the Virginia suburbs of Washington, where the President speaks in a town-hall meeting, during which Josh signals him that the problem with the shuttle has been resolved. Afterward, as the group returns to the motorcade, Zoey's Secret Service agent Gina Toscano sees something, but is unable to piece it together before two unknown concealed gunmen begin shooting. The screen goes to black, leaving the fate of the President and senior staff unknown.

• Aaron Sorkin
• Thomas Schlamme
• John Wells
• W. G. Snuffy Walden

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