When Will informs Dad that there isn't enough food for dinner, his father begins to ask Holly to gather more, but she immediately redirects the responsibility back to her brother. The two children begin an argument, which is halted only when Holly sees Dad trying to make soup out of a rock; they begin to worry if their father has flipped his wig. Dad explains with an air of seriousness that he's making Stone Soup, and asks his kids to try it. When Will and Holly insist that it tastes like hot water, Dad admits that it could use a little salt, but unfortunately they've run out. The kids kindly offer to fetch some right away, being concerned for their father's mental stability; they cheerfully recommend he take a rest until they return.

While out collecting salt chunks, Will strikes up a truce with Holly to ease the stress on Dad, which has increased during the drought. On their way back to the cave, the chronic lightning without rain has Holly speculating that someone could be messing with the weather pylon. Just then, a pack of dinosaurs (Emily, Spike and Spot) charge by, sending the kids for cover in the brush. Will notes that the giant lizards are probably searching for water, and that the Pakuni must have it rough since the dinosaurs have nearly stripped the Pakuni's territory clean of food. As the kids continue back, Ta and Sa enter a nearby opened pylon.

Dad tries out the salted soup, considering it satisfactory, but Holly points out its lack of nourishment. She suggests adding some carrots and turnips they've gathered that day (strangely, they're of normal Earthly proportions rather than the gigantic Land of the Lost variety seen in previous episodes); Dad, showing mock reluctance, agrees. Will adds that the soup could also use some onions and potatoes, asking Holly to help him find some. The children rush out to pick more vegetables, leaving Dad smiling.

Will and Holly find Emily feeding at their usual vegetable patch, leading Holly to grumble about it. Emily apparently takes offense and charges at the kids, but luckily Will and Holly spot the open pylon and take refuge within. Emily bellows just outside, nudging the pylon and almost tipping it over. The kids notice that the pylon is dark, but head out since the angry brontosaur has left.

Will and Holly bring in their harvest of vegetables, plus an iguana that Will has just caught. Dad says "yes" to the onions and potatoes, but "no" to the lizard. As they all sample the vegetable soup, Dad comments how it no longer tastes like a rock; the kids finally realize the well-intentioned con their father has pulled. Dinner is served.

During the night, Ta and Sa scurry through the jungle near the cave. Sa stumbles; her screech awakens Dad. The forest ranger peeks out of his cave to see the puzzling sight of Pakuni carrying light-crystals.

The next day, Will and Holly show their father the open pylon they found the day before. Dad concludes that the pylon is dead, since the crystals have been removed from the matrix. He does emphasize that the need to correct the problem soon, since the missing crystals could be the cause of the drought. As they head back to their cave through the rainless lightning (again the pink clouds look suspiciously like bubbling fog filmed upside down), the Marshalls run into Ta and Sa. Ta accuses the family of stealing the Pakuni's food, demands that Holly hand over her necklace, then orders the humans to leave. Back at their cave, Dad explains the Pakuni's inherent territorial nature; the family's presence is an intrusion on their turf. Will revisits the problem of the pylon, to which Dad says he may now know a solution.

Dad leads the children to the Pakuni Enclosure, where they begin to hear the familiar sound of energized crystals. Dad warns that a yellow crystal piled with enough others could set off a tremendous explosion. As they approach the compound's entrance, Holly becomes afraid, but Dad approaches sharpened-stick-wielding Ta and Sa with a peace offering of food. After a bit of discussion with Sa, Ta accepts the gift. Dad then offers to make everyone Stone Soup, to which Ta also agrees. Will quickly fetches a soup stone while the deal still holds.

The Marshalls begin preparing the soup, with Will first adding the stone. Cha-Ka offers no reply after tasting the bland water, so Dad suggests adding some salt. After Cha-Ka retrieves a bowl of the "opira", Holly next recommends an onion (she drops it in whole -- no wonder Will always complains about her cooking), but Sa doesn't appreciate the flavor so far (Will and Dad strangely refer to Sa as a "he"; I always thought that Sa was female). Will then adds some potatoes, followed by Ta's choice -- "aganka" (iguana).

The soup cooks on as the lightning grows fiercer. Ta comes back with a flowering cactus, whereupon Dad demonstrates the inedibility of the needles by sticking one into his tongue (did it ever strike anyone to just pick the needles off?). Ta tries it for himself, with result quite humorous to his Pakuni clansmen. He tries adding the blossoms to the soup, but Holly insists that flowers are to be worn. She places the blossom on Ta's head, much to the amusement of Cha-Ka and Sa; Ta has a different opinion, made clear when he pops it in his mouth.

When the soup is finally ready, Dad tries to bargain with Ta. He offers one bowl of soup for each light-crystal, but the Pakuni leader refuses, describing the crystals' magic powers in his own language. To the family's surprise, Ta would rather trade for a nearby rock laying upon the ground. Will doesn't understand at first, but Dad catches on: Ta wants to trade for the Soup Stone. Dad and Will quickly grab the baskets of crystals as the lightning worsens and rush out to return them to the pylon from whence they came; the frightened Pakuni huddle in terror in the roofed corner of their compound.

The Marshalls dash into the pylon in hopes of restoring both it and the weather (they must have refilmed this scene; the outside of the pylon is already wet). Dad carefully returns the crystals to the matrix, causing lightning as each one is set in. As they peek outside, Will fears that the end of the world has come, but to their surprise and delight, rain begins to fall. Their newfound joy is briefly threatened when Holly wonders what will keep the Pakuni from returning to steal the crystals again; her father alleviates her worries when he turns the pyramidal key above the doorway, sealing it off. With their mission accomplished, Dad asks whose turn it is to prepare supper; jokingly, Will hands him a stone for their soup.

The following day as Will prepares dinner, he discusses the drought with his father. Though it hadn't rained much, Dad believes the drought is coming to an end. Just then, Holly hears Dopey outside, finding him playfully chasing Cha-Ka. She scolds the baby dinosaur and takes the scruffy, dirtied-up Paku up to the cave to get cleaned off. After brushing his fur and showing him a mirror, Holly invites Cha-Ka to eat dinner with them. After burning his finger in the soup (he never even tastes it), Cha-Ka mutters "yechh" and decides to make it his preferred way -- Stone Soup (again, he never even tries the improved broth!)