Originally published as a free serial on his website, some readers requested Weir to make The Martian available on Amazon Kindle. First sold for 99 cents, the novel made it to the Kindle bestsellers list. Weir then sold the rights to Crown Publishing Group, and the print version (slightly edited from the original) debuted at #12 on The New York Times bestseller list.

In 2035, the crew of the Ares III mission to Mars is exploring Acidalia Planitia on Martian solar day (sol) 18 of their 31-sol expedition.

When a severe dust storm threatens to topple their Mars Ascent Vehicle (MAV), the mission is scrubbed. But as the crew evacuates, astronaut Mark Watney is struck by debris and presumed dead. With the MAV on the verge of toppling, the surviving crew take off for their orbiting vessel, the Hermes.

After removing the metal skewer from his abdomen, Watney cleans the wound, applies a topical anesthetic, uses surgical tongs to remove one last metal fragment, and staples the wound shut.

Lacking communication with Earth, his only chance of rescue is via the Ares IV mission, which will be landing 3,200 kilometers (2,000 mi) away at the Schiaparelli crater in four years.

As the mission's botanist and mechanical engineer, Watney is the lowest-ranked member of the crew, but his botany and engineering background give him the skills he needs to survive on Mars.

Being the mission's botanist, he improvises a garden inside the Hab utilizing Martian soil fertilized with the crew's bio-waste, and manufactures water from leftover rocket fuel. He then plants the crew's unused Thanksgiving dinner potatoes to supplement his food supply.

"I'm definitely going to die up here if I have to listen to any more of this disco music," Watney tells his video journal. "My God, Commander Lewis," he complains to his ABBA-loving crewmate, "couldn't you have packed anything from this century?"

On Earth, NASA satellite planner Mindy Park, reviewing aerial Hab images, notices moved equipment and realizes Mark is alive. NASA director, Teddy Sanders, publicly releases the news, though the Ares III crew (still on route to Earth) are not told so that they will remain focused on their mission. Sanders overrules Hermes flight director Mitch Henderson, who believes the crew should know.

Watney interacts with several real-life pieces of existing technology, including a real-life NASA probe: Mars Pathfinder. Using Pathfinder's camera and motor, he establishes rudimentary two-way communication with Earth, first using hand-written signs, and then sending and receiving ASCII in hexadecimal.