Part I
Set in the fictional West African nation of Kangan, Anthills of the Savannah begins with a meeting between the president and his Cabinet. The current government has been in power for two years following a coup that ousted the previous dictator. Three lifelong friends have taken on significant roles in the new regime. Sam is the president, Chris Oriko serves as the Commissioner of Information, and Ikem Osodi is the editor of the government-run newspaper, the National Gazette. Ikem, an intellectual and poet, is vocal about the need for governmental reform. Chris often acts as a mediator between Ikem and Sam.

Sam has become a leader who disregards his people, focusing solely on acquiring more power by any means necessary. Chris and Ikem realize that Sam is quickly transforming into a dictator. They initially supported his rise to power, even encouraging him despite his doubts about his military background being sufficient for such a significant role. Now, Chris and Ikem regret their earlier support and seek to manage Sam in their own ways. Meanwhile, Sam's obsession with power has made him paranoid and temperamental. When Sam decides he wants to be elected “President-for-Life,” a national referendum is called, but the region of Abazon refuses to participate. In retaliation, Sam denies the region access to water during a drought, expecting that the lack of resources will force the people to comply. When delegates from Abazon arrive in the capital seeking mercy, Sam suspects they are plotting an uprising. His paranoia further convinces him that someone close to him is aiding the rebellion.

Although Chris recognizes the danger Sam poses, he believes that remaining in his government position allows him to serve his country. Meanwhile, Ikem's editorials become increasingly radical, and Chris tries to persuade him to moderate his views.

Ikem has a girlfriend named Elewa, who is semi-literate and works in a shop. She is pregnant with his child. Chris's fiancée, Beatrice, is a well-educated woman who works as an administrator in a state office. She has known Ikem since their youth and works for Sam, giving her connections to all the major characters. She observes the government's actions and the responses of Chris and Ikem, feeling she is the only one truly sensitive enough to understand the situation. She expresses to Chris and Ikem that they are addressing the problem incorrectly because they are not genuinely connecting with the people and the land.

Part II
Sam orders Chris to dismiss Ikem from his role as editor, but Chris does something unexpected—he defies Sam's command. Sam suspects Ikem is linked to the "protest" by the Abazon delegates, though Chris knows this isn't true. Nonetheless, Ikem is dismissed and later speaks to a student group at a university. Known for his outspoken nature, he openly criticizes the government. He jokes about the regime minting coins with Sam's face, which is twisted into propaganda suggesting Ikem called for the president's beheading. Ikem is abducted from his home during the night and executed by the state police.

Part III
Chris realizes the extent of Sam's danger and goes into hiding. Using his connections in the international press, he exposes the truth about Ikem's assassination. With support from Emmanuel, a student leader who looks up to Chris; Abdul, a supportive cab driver; and a small covert network, Chris escapes the capital, Bassa, by bus and heads to Abazon. Meanwhile, the government issues an arrest warrant for Chris and threatens anyone withholding information about his whereabouts.

During the bus journey, Chris feels a renewed connection to his homeland, and Emmanuel meets a beautiful...