Black Wind opens in a Japanese submarine I-403 in World War 2. The submarine captain reluctantly takes on a doctor and a secret payload. Their plan, he learns, is to attack America with something called "Makaze," the Evil Wind. Once near American shores, though, a naval vessel destroys them.

More than sixty years later, the story opens on the Aleutian Islands where several scientists and meteorologists begin to experience bizarre health symptoms and die. Moments before three scientists are about to die, a man in a wetsuit, with green eyes, appears from the water. It's Dirk Pitt, Jr., and he arrives just in time to save the three scientists, one of whom is a beautiful woman.

On the mainland, everyone is checked out and given a clean bill of health. However, subsequent tests show the attack was cyanide poisoning. Pitt investigates instances of cyanide poisoning in the US and finds a link to a Japanese sub that attacked American soil during World War II. A friend discovers that several Japanese subs were sunk close to American shores, including the I-403, which was carrying a mysterious payload.

Dirk finds the I-403 and discovers the payload to be cyanide. After more research, he learns that there is another sub with more canisters of poison, the I-411. He boards a NUMA ship, checks out the I-411 and finds the canisters of poison intact. The NUMA ship, however, is taken over by a group of villains. Pitt and his sister are kidnapped and taken to Korea, where they meet the mastermind behind several killings, Kang. Kang admits that he plans to kill a lot of people with a super-virus he is concocting from the viruses and chemicals taken from the submarines. After revealing his plan, he plans to kill the Pitt siblings.

Dirk and Summer escape, make their way back to America, and reveal the plan to the authorities. With the help of NUMA, the Coast Guard, and the Navy, the West Coast is patrolled for any incoming Japanese or Korean vessels, but they find nothing deadly.

Meanwhile, Kang's group takes over a floating rocket launching platform, and they insert their super-virus into the rocket and plan to launch it over Los Angeles. There, it will wreak immediate havoc, but will also have a prolonged and terrible effect on the United States.

In a blimp, Dirk Pitt, Sr. notices that the former oil-drilling rig seems out of place. He learns they are not supposed to be there. Meanwhile, his son takes a prototype core-drilling machine and tries to stop the launch. Dirk Pitt Jr. is unsuccessful. His father, though, lands in the blimp, rescues his son and the sea launch engineers, and they leave in the blimp. Dirk Pitt, Sr., learning that the launch cannot be stopped, gets into the prototype core drilling submersible and drills holes in the pontoons of the sea launch platform, altering the angle of the rocket when it takes off. It splashes harmlessly in the water.

Pitt survives the chaos and resurfaces in the submersible. He is picked up in the blimp by his son, and they chase some of Kang's henchmen, stopping them. Then Dirk Pitt, Jr. accompanies a SEAL team to Korea, where they attack Kang's fortress. Dirk Pitt, Jr. ends up in a face-to-face battle with Kang. He wounds the villain and jumps off of the yacht, before it crashes and explodes. Then, he returns to America where he meets up with the beautiful scientist. They drive off into the sunset together.