The novel begins with a brief prologue describing the bioforms – dubbed the First-Born – who created the black monoliths. They evolved from "primordial soup", and over the course of millions of years, became a space-faring species. Perceiving that nothing was more precious than "mind", they catalysed the evolution of intelligent species wherever they went, by increasing the intelligent species' chance of survival. After visiting Earth, the First-Born found a way to impress themselves into the fabric of space and time, becoming effectively immortal. Meanwhile, the monoliths—implied to have been forgotten by their creators when they ascended to a higher state of being—continued to watch over their subjects.

3001 follows the adventures of Frank Poole, the astronaut killed by the HAL 9000 computer in 2001: A Space Odyssey. One millennium later, Poole's freeze-dried body is discovered in the Kuiper belt by a comet-collecting space tug named the Goliath, and revived. Poole is taken home to learn about the Earth in the year 3001. Some of its notable features include the BrainCap, a brain–computer interface technology; genetically engineered dinosaur servants; and four gigantic space elevators located evenly around the Equator. Humans have also colonised the Jovian moons Ganymede and Callisto. TMA-1, the black monolith found on the Moon in 1999, had been brought to Earth in 2006 and installed in front of the United Nations Building in New York City.