In the background to the story in the book, an ancient and unseen alien race uses a mechanism with the appearance of a large crystal monolith (black in the film adaptation) to investigate worlds all across the galaxy and, if possible, to encourage the development of intelligent life. The book shows one such monolith appearing in ancient Africa, three million years B.C., where it inspires a starving group of the hominid ancestors of human beings to conceive of tools. The ape-men use their tools to kill animals and eat meat, ending their starvation. They then use the tools to kill a leopard that had been preying on them; the next day the main ape character, “Moon-Watcher”, uses a club to kill the leader of a rival tribe. Moon-Watcher reflects that he is now master of the universe, but is unsure of what to do – but he’ll think of something.
The book then leaps millennia to the year 1999, detailing Dr. Heywood Floyd’s travelling to Clavius base on the Moon. Upon his arrival, Floyd attends a meeting. A lead scientist explains that they have found a magnetic disturbance in Tycho, one of the Moon’s craters. An excavation of the area has revealed a large black slab, designated Tycho Magnetic Anomaly-One (TMA-1). It is precisely fashioned and, at three million years of age, was not made by humans. It is the first evidence for the existence of intelligent life off the Earth. Floyd and a team of scientists drive across the moon to actually view TMA-1. They arrive just as sunlight hits upon it for the first time in three million years. It then sends a piercing radio transmission to the far reaches of the solar system.
The book then leaps forward 18 months to the Discovery One mission to Saturn. David Bowman and Frank Poole are the conscious human beings aboard Discovery One. Three of their colleagues are in a state of suspended animation, to be awakened when they near Saturn. The HAL 9000, an artificially intelligent computer, maintains the ship and is an active part of life aboard.
While Poole is receiving a birthday message from his family back home, HAL tells him that the AE-35 unit of the ship is going to malfunction. Poole takes one of the extra-vehicular pods and swaps the AE-35 unit, which is critical for sustaining communication with Earth. Bowman conducts tests on the AE-35 unit that has been replaced and determines that there was never anything wrong with it. Later, HAL claims that the replacement AE-35 unit will fail. Apprehensive, Poole and Bowman radio back to Earth; they are told that something is wrong with HAL and are given orders to disconnect him. These instructions are interrupted as the signal is broken. HAL informs them that the AE-35 unit has malfunctioned.
Poole again takes a pod outside the ship to bring in the failed AE-35 unit. As he is removing the unit, the pod, which he had left further from the ship, begins moving toward him. He is powerless to move out of the way in time and is killed by the impact; his spacesuit ripped open. Bowman is shocked by Poole’s death and is deeply distressed. He is unsure whether HAL, a computer, really could have killed Poole. He decides that he will need to wake up the other three astronauts. He has a long argument with HAL, with HAL refusing to obey his orders on the basis that he is supposedly incapacitated. Bowman threatens to disconnect him and HAL relents, giving him manual control over the process of ending the hibernation.
As Bowman begins to awaken his colleagues, he feels a cold chill; HAL has opened the inner and outer airlock doors to space, venting the ship’s atmosphere. The pressure on board is rapidly dropping as the ship is equalizing with the vacuum of space. Bowman makes his way into a sealed emergency shelter which has an isolated oxygen supply and spare spacesuit. He then puts on the spacesuit and re-enters the ship, knowing that the three hibernating astronauts are dead. Bowman then laboriously disconnects HAL, whom he now knows to be a murderer. Bowman puts the ship back in order and manually re-establishes contact with Earth. He then learns that the true purpose of the mission is to explore Japetus (the third-largest moon of Saturn), and contact the society that buried the monolith on the Moon.
Bowman learns that HAL had begun to feel guilty and conflicted about keeping the purpose of the mission from him and Poole, which ran contrary to his stated mission of gathering information and reporting it fully. This conflict had started to manifest itself in little errors. Given time, HAL might have been able to resolve this crisis peacefully, but when he was threatened with disconnection, he defended himself, because his very existence was at stake.
Bowman spends months on the ship, alone, slowly approaching Japetus. A return to Earth is out of the question, as HAL’s sudden decompression of Discovery severely damaged the ship’s air filtration system, leaving Bowman with far less breathable air than either returning to Earth or waiting for a rescue ship would require. Hibernation is impossible without HAL to monitor it. During his long approach, he gradually notices a small black spot on the moon. When he gets closer, he realizes that this is an immense black monolith, identical to TMA-1, only much larger, which the scientists back on Earth name “TMA-2”. The name is doubly inappropriate: this object is not in the Tycho crater and, unlike its lunar counterpart, it has no magnetic field.
He decides to go out in one of the extra-vehicular pods to put down on the monolith. The monolith, which had been inert for so long, opens and swallows Bowman’s pod as he proclaims: “The thing’s hollow — it goes on forever — and — oh my God! — it’s full of stars!” Mission control never hears from Bowman again.
Bowman moves very quickly through a field of stars that seem to have no end emerging in a star system far outside our galaxy. Eventually, he is brought to what appears to be a nice hotel suite, carefully constructed from monitored television transmissions, to make him feel at ease. Bowman goes to sleep. As he sleeps, his mind and memories are drained from his body. David Bowman is made into a new, immortal entity that can live and travel in space; a Star Child. The Star Child then returns to our Solar System and to Earth, where it detonates a nuclear missile while it’s in flight and saves millions of lives. It then reflects that it is master of the universe, but is unsure of what to do – but it’ll think of something.