The USS Enterprise is exploring the center of the galaxy, looking for the heart of creation. When the ship is caught inside a tornado made of pure energy, a devil like being calling himself Lucien appears to save them. Lucien takes Capt. Kirk and his crew to the magical planet of Megas-Tu. But when the Megans discover the presence of humans, they put them on trial the same way they were treated when they visited Earth centuries earlier.
The Enterprise crew runs into its old nemesis; Harcourt Fenton Mudd, more commonly known as Harry Mudd. Time's not changed Mudd's predilection for nefarious business ventures. This time, he's peddling an illegal love potion. The drug does have an accidental effect; on Spock, who, again finds himself falling for nurse Christine Chapel.
While on a mapping mission, the Enterprise receives an outdated transmission from the volcanic star Cepheus. A flash of light from the planet passes through the ship and disables all dilithium crystals. Soon thereafter, the crew begins to shrink. With no cure in sight, it becomes increasingly difficult for the Starfleet officers to handle the ship's controls.
A team comprised of various intergalactic experts, amongst them are Kirk and Spock, must recover an artifact known as the Soul of the Skorr. The theft must be kept secret, or a galactic holy war could break out.