While Will makes dinner, Holly compliments his wonderful cooking in an attempt to get him to do her share of meal making. Her comment starts a friendly battle of the sexes, this time over which gender makes better chefs. Dad, who is working on their cloth map of the Land, puts a quick end to his childrens' argument. Holly then directs her attention to Dopey, who is whining for attention outside, and warns the grazing brontosaur against nibbling in the Marshall's garden. When the pathetically tacky prop of the baby dinosaur's neck and head whines with its mouth full of fern leaves, Holly can hardly keep from bursting into laughter. (Out of all the tacky scenes of involving the foam prop of Dopey's head, this one definitely has to be the worst.) As she strolls back into the cave with a stupid smirk on her face, she explains to Will that this evening's near-approaching sunset should be quite beautiful. Meanwhile, a pylon's matrix table "blows a fuse" (one of the crystals "burns out"), smoking after all the crystals go dark (apparently they must all be there in an appropriate arrangement to give off a resonating glow).

While eating dinner, Holly complains that there is an unusual amount of ruckus coming from the dinosaurs in the jungle. When she hears Grumpy's roar approaching, she dashes out to warn Dopey; during the brief moment outside, she notices that the almost-setting sun appears to be in exactly the same position as it was as while ago. Will questions his sister's observation, but Dad, glancing at his watch and seeing the amount of light left outside, acknowledges that something is wrong. He steps out of the cave entrance for a moment to look for himself at the sun over the unusually noisy jungle, where the view confirms his suspicion. He likens the phenomenon to time standing still, whereupon Holly concludes that the unset sun must be what is inciting the dinosaurs to such chaos (recycled dinosaur animation clips are shown). Dad is at a loss to explain what is happening, but suggests that Enik may have a clue. Will wants to join his father, but Dad considers it too dangerous. He does agree to wear one of Holly's clairvoyant pendants, and hastily bids farewell as he heads out for the Lost City.

In the Library of Skulls, the net-wielding Sleestak peer into a smoking urn. After misty images of the ancient Altrusian civilization appear (apparently shown to define the origin of the Library's knowledge), they witness a vision of Rick Marshall and his two children opening a pylon in the jungle. The Sleestak nod to each other and head out with the net. Dad arrives in the time doorway chamber, but Enik does not answer his calls; Dad is pursued by Sleestak (associated with corny music in the 2nd season) as he searches the nearby tunnels. Holly luckily checks up on Dad that very moment through her magic pendant, witnessing her father's capture. Will urges that they go immediately to Dad's rescue, so the kids rush out of their cave and hurry through the jungle. With Dad entangled in their net, the Sleestak bring him to the Library; Will and Holly check on Dad's location with the pendant during a brief rest. Thinking to himself, Dad fights to stay awake as the mystical smoke begins altering his consciousness. Still viewing Holly's magic pendant, Will guesses that their father has been taken to some kind of temple. Holly worries how they will find this new place; her brother can only reply that they will have to search all over the Lost City.

As the Council gathers together, the Sleestak Leader (identified by a ceremonial pendant) addresses the Index Skull, first asking of their race's destiny. The skull booms out that they are 7000 strong with all of their eggs fertile; they cover the land and are universally feared. Dad is quite surprised that he can understand the Sleestak, and assumes it is a result of mental connections via the special smoke. The Leader seeks permission to question the Index Skull, but is required by ritual to first reference history. In a feeble, venerable voice, the Skull of History grants permission to question, but is interrupted by their captive. Dad declares his non-adversarial position, but the Sleestak Leader commands silence. The Leader explains to the aged skull how the sun does not set, and how it prevents their hunting of the sacred Altrusian Moth. When he asks the skull to retell how their enemy caused the event, Dad proclaims his innocence, but again the Leader demands silence, stating that the vision will prove his guilt. After they all review a scene of Rick Marshall entering a pylon, Dad realizes the nature of the charges brought against him; he is accused of stopping the sun from setting by tinkering with the pylon's controls. Dad maintains his innocence, but the Leader insists the Skulls do not lie; the Leader holds his captive responsible for any stillborn deaths caused by his race's postponed hunting. Dad complains about the unfairness of his "trial", so is granted the right to speak (up until now, Dad communicated solely through telepathy). When he asks about the age of the Library's skulls, the Leader responds "they have always been here; all things from Altrusia come from here. They are never wrong, and you must DIE." Dad insists he has not gone into the pylon, but agrees that it was him in the vision; the Leader considers the acknowledgement a confession of conspiring to destroy his race, but Dad regards the vision as a prophecy. He tries to persuade the Sleestak that what they saw were instructions to resolve the problem rather than evidence of a crime, and questions the validity of the interpretation of the Skulls' knowledge throughout the past thousand years. The Leader is unable to rebut Dad's charge, and after consulting with the Council, denies their captive's request to be released to enact the scenes seen through the smoke. Dad demands that the Leader directly consult the Skulls to indisputably establish his innocence, but after another incomprehensible discussion with the Council, the Leader considers it unnecessary ("we already know you lie", he insists.) Dad's fate appears to be sealed when the Leader announces that the Council will now schedule the time and place for him to join the skull of his father.

Will and Holly arrive at the Lost City Plaza, where they quickly dash into the tunnels to escape from Big Alice, who has just returned from the jungle. They don't make it very far in before they are chased out by the Sleestak; the angry creatures fling a net at the kids but retreat due to the blinding sun. Will then proposes that they try the west entrance, since the Sleestak won't bother them there; the perpetually almost-set sun will shine directly into the tunnel. The kids rush on to save their imprisoned father.

Will and Holly reach the Library of Skulls, unnoticed by the Sleestak. Holly immediately begins to feel the strange effects of the smoke. Dad, who is trying fruitlessly to win judgement directly from the Skulls, spots his two children and commands them to flee. The kids foolishly react slowly to the warning, and in no time are surrounded by Sleestak.

All of the Marshalls' hands are tied as they await their fate. Dad assures his children that he will think of some plan of escape, but the effects of the smoke grow stronger; his eyes are droopy, his speech is slurred, and he begins to see hallucinations. Holly and Will appear to shrink away from him though they stand right near him all the while. Dad proposes they use his knife to cut themselves free, but Holly reminds him that the Sleestak had taken it away. He instructs Will to reach into Holly's back pocket to get the crystals she brought along; he then directs his son to create a diversion by dropping the crystal into an urn. When the crystals are placed into the urn, it begins to spark and smoke, giving them the perfect opportunity to escape. Will and Holly begin to exit, but Dad is distracted by a vision of a wavering green light; not until after the diversion is over does he tell his children to run. The Sleestak are momentarily blinded by the "short-circuiting" urn, but the Marshalls wait until after that to flee. The sluggish Sleestak are slow to react; a skull commands them to recapture their prisoners.

The next thing we know, Dad leads the family calmly down a passage; though the childrens' hands are still tied, his have been cut free. He stops his kids to witness another wavering green vision, this time he sees a view of Earth. Will explains that nothing is there, after which he and Holly inexplicably wander off (or at least fail to follow their father). Dad hallucinates a scene of the family as neanderthals by a campfire; meanwhile, the Sleestak pursue him through the tunnels. He then is spoken to by a colonial-era Holly, but the image quickly disappears. Dad calls out for his children, when Will, in military dress uniform, marches silently by. As his son tramps away, the Sleestak advance slowly toward Dad down the clean, flat, unnatural passage. Dad runs down the passage and reaches the west entrance, but the Sleestak catch up to grab him. As the effects of the smoke wear off, it becomes clear that the "Sleestak" are actually Will and Holly. Dad comments how they were lucky to escape from the Library of Skulls, but his children don't know what he is talking about; they insist they just started heading into the west entrance when their father came running by. Dad describes how he was held prisoner, and that his knife had been taken away; he is unable to explain how his hands were cut loose, a fact that enabled him to escape. He assumes he had made a bargain with someone, and so leads everyone to a pylon ("a clock for the Land of the Lost", he postulates) that they recently mapped in the jungle.

After opening the pylon, Dad tells Will and Holly to stay outside. He steps up to the matrix table, then returns to the doorway by the kids. He asks Holly for a blue crystal, explaining that he saw himself do this in the smoke in the Library. When Dad replaces the burnt-out crystal with the "fresh" one from Holly's pocket, the matrix table immediately lights up and begins to hum softly. As he leaves the pylon, the sun quickly sets on the horizon.

On their way back to the cave through the jungle twilight, the Marshalls encounter Sleestak wielding nets. To the family's surprise, the Sleestak continue on, hunting their sacred Altrusian moth. Will discovers that they returned Dad's knife, having stuck it into a nearby log. Will reconsiders his attitude toward the Sleestak; at least for that night, they have made peace.