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The President vetoes his first bill—the repeal of the estate tax—and staffers scramble to counter the GOP's override threat, first having to deal with an opportunistic Democratic congressman before Sam has an idea that leads them to a surprising ally. An international crisis erupts when Palestinian terrorists kill two Americans in Israel. Meanwhile, Charlie has been offered legal immunity and everyone urges him to take it, and a reporter mocks C.J. but is later humiliated by her in response.

The President asks a reluctant Vice President (Tim Matheson) to speak at an anti-gun rally in Texas after a church shooting, while Donna goes before a Congressional committee investigating President Bartlet's lack of disclosure and lies under oath when her new boyfriend asks her a personal question. Toby deals with a leaked quote that is embarrassing to the President, while C.J. meets up with a gutsy reporter and Sam ponders a plan to eliminate the penny.

An American spy submarine suddenly goes silent in hostile waters outside North Korea, and President Bartlet must decide whether he should notify the enemy or attempt a risky, secret rescue. Meanwhile, a top Republican contender cannot articulate why he wants to be President, but C.J. is disappointed with President Bartlet's own answer to that question. Toby clashes with a Congresswoman over funding the National Endowment for the Arts.

On the day before Thanksgiving, the President is talking turkey to whoever will listen (and everyone must). Meanwhile, C.J. deals with two Native Americans who have encamped in the lobby. Toby annoys the President when he finds out polls involving the First Family increase his popularity. Sam is dismayed by a new formula for poverty and Josh goes diplomatic on a case involving a Georgia teen who killed his teacher and fled to Italy.

C.J. argues with senior staff over whether to make public the possibility of an outbreak of mad cow disease, as well as the renewal of a lease on a Qumari military base despite her horror with that nation's treatment of women. Toby meets with veterans upset about the content of a Smithsonian Pearl Harbor exhibition, and Josh finds some sparks when he meets with a woman's group director named Amy Gardner.

It's Christmas, and the most pressing matter is a threat to firebomb black churches in Tennessee on Christmas Eve. Leo testifies before a Congressional committee on the MS matter, recalling several critical moments from the Bartlet campaign and a personal slip-up that could end his career and badly damage the President.

Leo defiantly rejects the Congressional committee's offer of a public censure of President Bartlet that would end the investigation into his concealment of his illness and spare Leo any possible personal repercussions, while the President continues to weigh his options. In other stories, Josh puts his foot in his mouth over his courtship of Amy, Sam is angry over a White House tell-all book, and Charlie's heartfelt purchase of an old Middle East map for the President leads to some political problems.

While the White House staff works intensely on the President's State of the Union speech, President Bartlet and the First Lady have dinner with a group of her scientist friends who speculate that sphingosine kinase could lead to a cure for cancer. As a result, the President demands that a passage ambitiously promising a crusade to cure cancer within ten years be included in the speech. Sam is the point man for the speech, which is billed as the most important of the President's career and one whose failure could end his hopes for re-election. As Sam is very reluctantly interviewed for a Vanity Fair profile by Lisa Sherborne, who was once his fiancée, he lays out the process by which a State of the Union address comes about. Sam knows that the pledge to cure cancer is noble and the kind of over-reaching government should do, but also that for political reasons it cannot be included in the final speech and removes it. He takes out most of his frustrations on Lisa who finally tells Sam she is taking herself off the story, reminding him that it was he and not her who ended their engagement. Attracted to Amy Gardner, a prominent women's rights leader, Josh tries to persuade her that her burgeoning romance with a Congressman is solely a result of political machinations.

The staff debates whether to counter a fast-rising Republican presidential candidate's verbal assault on affirmative action at the Iowa caucuses and Josh postpones his tropical vacation with women's rights advocate Amy Gardner to defuse a risky situation in Vieques, Puerto Rico. C.J. surprises Toby with her lack of enthusiasm for affirmative action, while Sam has to meet with a UFO crackpot per Leo's orders. Toby and President Bartlet clash over the President's mental state and relationship with his father.

President Bartlet consults Dr. Stanley Keyworth for a troubling sleep disorder and receives a sobering personal assessment. C.J. lobbies vigorously to help secure the release of a White House reporter who has been taken hostage while on assignment in the Democratic Republic of the Congo. Toby clashes again with his ex-wife over a speech for the United Nations that takes radical Islam to task. Sam is accused of sexism by a young intern but Ainsley comes to his defense.

President Bartlet engages both Sam and Toby in intricate chess matches that mirror the wily game of brinkmanship that Bartlet is playing with the Chinese, who are conducting war games in the Taiwan Strait. The small New England town of Hartsfield's Landing kicks off voting in the New Hampshire primary, and Josh is lobbying for every vote he can get. A prank war between C.J. and Charlie turns somewhat destructive.

As Abbey contemplates the possible loss of her medical license, she grudgingly attends a White House party for her birthday. Toby discusses the inclusion of a Sinn Féin member in the guest list of a White House event with British Ambassador Lord John Marbury (Roger Rees). Sam gets another visit from someone who wants to give him orders about what to do, this time from a respected former teacher of his who wants the US to fund a major scientific research effort. Donna's US citizenship is called into question.

When a truck carrying uranium fuel rods crashes in a remote Idaho tunnel, President Bartlet's staff prepares for a potential environmental or terrorist crisis. Donna seeks a presidential proclamation honoring the retirement of her favorite teacher. The staff considers removing Vice President John Hoynes from the ticket but for different reasons; Sam and the President are not going to let that happen.

As Sam is finalizing the details of President Bartlet's upcoming summit with the Russian president, satellite photographs reveal an Iranian nuclear bomb facility being built using Russian technology. During a press briefing, C.J. voices her personal indignation that a group of schoolgirls in Saudi Arabia were prevented from escaping a burning building by religious police because they were not dressed properly according to Sharia law. After receiving death threats, C.J. is assigned Secret Service Special Agent Simon Donovan (Mark Harmon) for personal protection, and he tells her that the individual who is targeting her has no connection to jihadists. Toby tries to help a Russian journalist he thinks is being suppressed by her government, and Charlie unravels a mystery involving a long-lost letter to Franklin Roosevelt.

While C.J. gets used to being tailed by Special Agent Donovan, the President must deal with a terrorist threat on a military installation that gets closer and closer to home and leads to a frightening revelation. Meanwhile, Toby plays hardball with network TV executives who want to cut national convention coverage, and Sam's plan to keep dirty tricks out of the presidential campaign blows up in his face.

President Bartlet agonizes over whether to disregard the principle of diplomatic immunity for a Middle Eastern official who is known to be plotting terrorist acts. The President is advised not to attend a fundraiser for a politically sensitive cause because his Republican opponent will also be attending. Josh and Amy clash over a welfare renewal bill, while Sam is gun-shy after the tape disclosure from earlier. Note: The episode title refers to the U.S. military assassination of Admiral Isoroku Yamamoto in 1943.

President Bartlet makes a life-or-death decision regarding the defense minister of Qumar who is a known terrorist. The flirtation between C.J. and her Secret Service bodyguard, Simon Donovan, is limited by their professional relationship and then cut short by tragedy. Josh defeats Amy in the welfare bill battle and their relationship is left with an uncertain future. President Bartlet encounters his opponent, Governor Ritchie, at a performance of The Wars of the Roses.

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