On Madam Secretary Season 2 Episode 1, Air Force One goes missing and the line of succession is called into play. Unfortunately, the Vice President is in surgery, the Speaker of the House is on the missing plane and the Senator who was next in line is not in his right mind. Elizabeth is quickly sworn in, but Russell makes sure she knows it's not permanent. While being sworn in, Elizabeth finds out the National Security Advisor is leaving and she had no knowledge of it. She finds out from Russell that the President has already picked the next National Security Advisor and she is visibly angry over and doesn't understand why she didn't have a say in it.

Eventually Air Force One is found and they quickly learn the communications went down, but everyone on the plane is fine and accounted for. Once the plane lands, they investigate what went wrong and at first solar flares are blamed for Air Force One being down, but Elizabeth is called in later in the evening and told there was a sophisticated virus uploaded onto Air Force One and that's what caused it to go dark. Elizabeth immediately realizes there is someone who is wanting to declare war, but they just need to find out who it is.

Meanwhile, Henry is reluctantly working with the DIA who wants him to recruit one of his students as a spy for the NSA. Henry isn't comfortable with blackmailing his student and he comes up with an alternate person for the DIA to go after, but is surprised to learn they want him to be the students handler.

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