As Mackenzie begins the transition into the office of President, she has to select a Vice President, a situation in which Nathan Templeton tries using to his advantage. Mackenzie's daughter, Rebecca, faces a crisis when her diary goes missing, which contains information about her mother that could hurt her.

Faced with her first national crisis - the death of nine DEA agents in Latin America - Mackenzie shows strength and resolve in dealing with a corrupt leader. Meanwhile, Nathan Templeton is approached by an ambitious congressman who served with Mac's Vice Presidential candidate, Warren Keaton, and is eager to divulge potentially damaging info in an effort to derail his nomination. Mac's teenage twins resume public school, only this time it's complete with secret service detail and press spectacle, and while popular Horace welcomes the attention, shy Rebecca finds it overwhelming.

In the middle of the announcement of her new National Security Advisor, Anthony Prado, Mac is caught off guard by the breaking news of a terrorist smuggling explosives across the Canadian border. The way in which Mac and her Attorney General deal with the situation pits them squarely against each other, and Nathan Templeton takes great pleasure in publicly second-guessing Mac's every move. Meanwhile, it's Halloween, and Amy - who desperately wants to go trick-or-treating like a normal kid - is disappointed to learn that, due to security concerns, she may have to settle for a party this year instead. When Rod as First Gentleman finds himself fodder for late-night comics, it hits his son Horace especially hard.

When a tell-all book is published about Mackenzie Allen that contains confidential information suspicions arise. Meanwhile, the confirmation hearings for Vice Presidential nominee Warren Keaton begin, but raise questions about his past.

After she announces new direction for her administration, President Allen finds herself in need of allies within the West Wing and decides that she needs to appoint her closest adviser, Rod, to an official position.

While trying to coordinate the rescue of the crew of a damaged U.S. submarine off the coast of North Korea with help from Chinese, Mac must deal with war fever among her advisors and a leak from China to the North Korean government that threatens to start a nuclear war. Meanwhile, Speaker Templeton’s wife secretly encourages Jayne Murray to accept Nathan’s offer to rejoin his office as chief of Staff.

Mac decides to stand by her friend and Attorney General nominee, Carl Brantley, after he gets hammered in his confirmation hearings. A cargo plane which contains military weapons goes missing over Pakistan and it's up to Vice President Keaton to resolve the situation. Meanwhile, Rod tries to settle in the domestic life, but soon faces a crisis when Kate is nowhere to be found.

Mac suffers a burst appendix while aboard Air Force One. Since there is no Vice President in place, Templeton becomes acting President since he is the Speaker of the House and next in line. Meanwhile, there is an air strike that is crippling travel on Memorial Day weekend and Templeton ends up overstepping his bounds and handles the situation the way he wants to.