Kirk is leading a survey party on a planet he once explored as a Liutenant aboard the U.S.S. Farragut in 2254. He is surprised to see the inhabitants armed with flintlock-style guns and intervenes to stop them from ambushing an old friend of his called Tyree. The landing party is pursued and Spock is shot before they manage to beam back up to the Enterprise. A Klingon vessel is detected in orbit around the planet and Kirk orders Chekov to keep out of their sensor range while they find out what it is up to as he suspects that the Klingons have something to do with the planet's speeded-up development.

In sickbay, M'Benga and McCoy have done all they can for Spock who has gone into a Vulcan healing trance. Kirk takes McCoy with him back to the surface to try and find some solid evidence of Klingon interference in the planet's development. They are attacked by a white, horned, ape-like creature called a Mugato which bites Kirk before McCoy can destroy it with his phaser. The creature's bite is poisonous but McCoy is unable to summon help as the Enterprise has moved out of communication range.

Hill people find the pair of them and take them to their caves where Kirk discovers that Tyree is now their tribal leader. He is married to Nona, a Kahn-Ut-Tu witch woman who, Tyree believes, has a cure for the Mugato bite. Nona is keeping Tyree besotted with her by the use of drugs and keeps urging him to acquire 'fire sticks' for their tribe, which he refuses to do. On hearing of Kirk's arrival she heads for the caves, getting there just in time to see McCoy using a phaser weapon to heat up some rocks to keep Kirk warm.

She refuses to help Kirk until Tyree tells her all about them. Nona uses a living Mahko root to help heal Kirk, which involves cutting her hand and mixing her blood with his, holding the Mahko root between the wounds. Legend says that a person thus treated will be unable to refuse the healer anything. Tyree and McCoy sleep, waking later to find a cured Kirk sitting next to the sleeping Nona. On board the Enterprise, Spock's healing is also progressing. M'Benga tells nurse Christine Chapel to stay with him as he will soon be waking. When he does, he tells her, she must follow the Vulcan's instructions no matter how strange they may seem.

Planet-side, Tyree tells Kirk that the 'fire sticks' have been around for about a year or so but the villagers must make them by themselves as no strangers have been seen around. Kirk persuades Tyree to take them on a reconnaissance mission into the village. Nona also tags along, trying to persuade Kirk to help Tyree become more powerful. Kirk refuses to do this as he knows that his friend is basically a pacifist and is against killing people. Once in the village they locate a forge in which they find a chrome steel drill and some virtually carbon-free iron which is the evidence they need to prove Klingon involvement.

They move into hiding as a Klingon enters the forge with the village leader, Apella, and proceed to discuss the manufacture of improved weapons. McCoy and Kirk jump them and disable them for long enough to allow them to escape, taking one of the flintlocks with them. Back on board the Enterprise Spock starts to wake. Following his orders, Chapel starts to slap him to help him regain full consciousness. McCoy walks in and drags her off in disbelief at what he sees. Fortunately, M'Benga returns and continues hitting Spock until he is back to normal, fully healed.

Kirk shows the hill people how to use the stolen gun but Tyree doesn't want to know. McCoy questions Kirk's decision to give the hill people weapons but cannot supply an alternative suggestion to restore the status quo. Nona tries to use the same drug on Kirk that she is using on her husband but Tyree sees what is happening. He aims the gun at her but finds he is unable to bring himself to shoot her. A Mugato attacks and Kirk destroys it with his phaser. Nona knocks him out and grabs the weapon, running off and taking it to the villagers, offering them victory over the hill people in exchange for power, but they attack her.

Tyree, McCoy and Kirk reach them, but not in time to stop one of the villagers from killing her. Grief-stricken, Tyree picks up a gun and tells Kirk that he wants more weapons. Fortunately, McCoy has the presence of mind to retrieve the stolen phaser. Not for the first time does Kirk flout the Prime Directive, and orders Scotty to manufacture a hundred flintlocks for the hill people, putting them on an even footing with the villagers.