The crew arrives to find Earth in turmoil, threatened by a deep space probe that has drained all power and is vaporizing the oceans, producing a worldwide cloud cover which begins to block the sun. Because of the enormous storms ravaging the entire planet, Starfleet warns all approaching spacecraft to keep their distance.

Spock manages to identify the probe's unusual communication, which turns out to be a transmission to long-extinct humpback whales. When the probe's signal is not answered, it increases its output, causing more clouds and even more storms. Kirk and crew, orbiting the doomed planet, decide that the only way to save Earth is to time-travel back to the twentieth century, when whales still existed, and return to the present with a pair of the mammals. With any luck, then the probe's signal might be answered and Earth spared.

The crew, still piloting the Bird-of-Prey, use the slingshot effect to travel back in time. They pick up whale songs emanating from the West Coast of North America. They land the Klingon warbird in a San Francisco park, where thanks to its cloaking device, the ship is concealed from view. However, the time traveling damaged the ship's valuable dilithium crystals. The small crew then splits up, with Uhura and Chekov assigned to locate an atomic reactor for photons to recharge the ship's power, and McCoy, Scotty and Sulu ordered to create a tank in the cargo bay that will safely house a pair of whales.....