The book depicts the arrival of members of an alien species called the Fithp that have traveled to our solar system from Alpha Centauri in a large spacecraft driven by a Bussard ramjet. The aliens are intent on taking over the Earth.
Physically, the Fithp resemble man-sized, quadrupedal elephants with multiple trunks. They possess more advanced technology than humans, but have developed none of it themselves. In the distant past on their planet, another species was dominant, with the Fithp existing as animals, perhaps even as pets. This predecessor species badly damaged the environment, rendering themselves and many other species extinct, but left behind their knowledge inscribed on large stone cubes (called Thuktunthp, plural of Thuktun in the Fithp language), from which the Fithp have gained their technology. The study of Thuktun is the only science the Fithp possess. The Fithp are armed with a technology that is superior rather than incomprehensible: laser cannon, projectile rifles, controlled meteorite strikes to bombard surface targets, lightcraft surface-to-orbit shuttles the size of warships, etc.
The geopolitics of the world in this novel are those of the Cold War, although the setting of the story is in the mid-1990s. This affects the plot, since in the world of Footfall, the U.S.S.R. is still a major world superpower, and has a greater presence in space than the United States. At the time of the novel's writing, this was an extrapolation of contemporary trends.
The Fithp are herd creatures, and fight wars differently than humans. Throughout their history, when two herds met, they would fight until it was evident which one was dominant over the other; then fighting ceased and the losers were incorporated into the winning herd. The Fithp expect their contact with humans to proceed along these lines, and are confused by human attempts at peaceful contact. Upon arrival, they immediately attack the Russian space station, where Russian and Americans wait to greet them, without warning. Then they proceed to destroy military sites and important infrastructure on Earth. A US Congressman and Russian cosmonauts are captured from the ruins of the space station.
The novel's human characters fall into two major groups, those on Earth and those who are taken aboard the Fithp spaceship as captives. Civilians are used to show the effects of the war on day to day life in the United States, while military and government personnel convey a more strategic overview of events. Science fiction writers are employed as technical advisers on alien technology and behavior; these characters are based on real writers, including Niven ("Nat Reynolds"), Pournelle ("Wade Curtis"), and Robert Anson Heinlein ("Bob Anson").
Facing possible extinction due to the long-term effects of biological weapons, a group of high-ranking Fithp were selected by wager to escape to the stars. The Chtaptisk Fithp ('Traveling Herd') are divided between 'Sleepers' and 'Spaceborn', as the ship is both a generation ship and a sleeper ship. The original leaders of the herd are subordinate to their descendants the spaceborn, who are well prepared to start a space based civilization, but are still dedicated to the generations-old ideal of conquest.
After their initial assault, the Fithp land ground forces in and around Kansas. They defeat efforts by a National Guard detachment (and, somewhat later, three American armored divisions) to dislodge them by the using orbital lasers and barrages of kinetic energy weapons, but a combined Russian and American nuclear attack wipes out their beachhead. The Fithp, who are familiar with nuclear weapons but prefer to use cleaner ones, are shocked by what they consider the barbarity of humans' willingness to "foul their own garden" with radioactivity. Human protagonists, however, are exultant with victory.
It is during this initial invasion that more captives are taken. These also comprise a mixed bag of civilians including an elderly couple from the US Bible Belt and a mentally ill woman. These are put to work by the Fithp on board their mothership, who expect them to integrate themselves into the herd. The humans decide to cooperate until a chance for some serious sabotage presents itself.
The Fithp respond to the defeat of their invasion by dropping a "dinosaur killer", a large asteroid whose impact results in environmental damage on a global scale, in particular the almost total destruction of India. In the aftermath, the aliens invade Africa, where they enjoy more success. One result is the end of South African Apartheid (at much the same time, though in a completely different way, from how it would happen in actual history). Simply, Whites and Blacks become equal under the rule of the Fithp.
The United States secretly builds a large, heavily armed spacecraft propelled by nuclear bombs (a real concept commonly known as Project Orion). While an earlier implementation of the idea was ruled out due to environmental reasons and the danger of radioactive contamination, in the desperate situation facing humanity such considerations are cast aside. The ship is named after the Biblical archangel Michael, who cast Lucifer out of Heaven.
The Michael launches and battles through small enemy "digit" ships in orbit. Though seriously damaged, she pursues the alien mothership. One of the space shuttles carried aboard the Michael rams the Fithp ship, slowing it down enough for the Michael to catch and attack it.
There follows on Earth a confrontation between the American President David Coffey (loosely modeled on Jimmy Carter) - who is willing to make a compromise with the Fithp and let them withdraw into space, and who is reluctant to destroy their ship with their females and young in it - and his hardliner National Security Adviser, Admiral Carrell, who insists on unconditional surrender. Carrell effectively stages a bloodless coup d'etat, neutralizing the President and taking charge of the fighting in space.
The book clearly presents Carrel's unconstitutional act as justified: the compromise which the President was willing to accept would have left open the possibility of the Fithp making a new attack later. But with their ship (and most of their population) on the verge of destruction, the Fithp accept humanity as the stronger species and surrender themselves to become part of the human "herd".