The carefree Pakuni clan is feeding on wild grapes in the jungle when Cha-Ka notices a humming pylon nearby. Curiously but cautiously he approaches the structure, followed by Ta and Sa. Cha-Ka and his companions soon begin caressing the pylon's surface, which Will described earlier as feeling like "touching nothing". Suddenly, the exact conjunction of the three moons in the sky causes the pylon to open, luring curious Cha-Ka in; the entrance promptly seals off behind him. Inside, Cha-Ka stands before a crystal matrix table and a large, eerie-green viewing sphere, where he experiences a seizure as a strange, green energy covers his body. A glowing baton can be seen tumbling through space in the viewing sphere, and it suddenly appears in the hand of the now motionless Paku. Cha-Ka is somehow teleported out of the pylon, where he stands possessed before Ta and Sa with eyes glowing and face devoid of expression. When he stiffly directs the wand toward his cowering clansmen, it jolts them, after which they flee in terror. The Paku staggers zombie-like through the jungle, across the crevasse, and over to the Lost City, but is deterred from entering by Big Alice.

With her pudgy pal Dopey pulling the vegetable cart, Holly heads out into the jungle, promising she won't be out long. Though Will is concerned about her safety, Dad acknowledges that she's growing up, and besides, Grumpy went crashing off to the other side of the jungle earlier that morning. Dad heads out to do a chore himself, since the water jugs need refilling. Holly strolls along with Dopey, warning him not to eat up all the strawberries this time, when she comes across Cha-Ka. Foolishly, she assumes the Paku is offering the wand to her and reaches for it; as the baton is exchanged, so is the strange energy it bears. Holly is now possessed, while Cha-Ka tumbles back from its release and eventually escapes.

Will is busy cleaning his binoculars when Holly wanders into the cave. Her brother is quick to see that something is wrong, since she fails to respond, meanwhile using the wand to drain the various crystals laid out in their cavern. Each time the baton absorbs a jewel's energy, the device's hum rises in pitch. Will demands an explanation from his sister, but instead receives a shocking burst from her wand which knocks him out. After she finishes drawing the power from the remaining crystals, Holly abandons her unconscious brother and heads out.

When Dad returns with full water jugs, he rushes to his son's side. Luckily, Will wasn't seriously hurt, and explains what had happened. Before Dad can run after her, Will insists on going too; he can help locate Holly, since he claims to somehow be tuned into the wand's power.

Out in the jungle, Will detects an energy source, which perplexing to him and Dad, turns out to be Cha-Ka. Their Pakuni friend stumbles over to the men, but fails to respond when Will tries to fill his palm with a drink of water from his canteen. Dad guesses that Cha-Ka is in a state of shock, and directs him home to Ta and Sa. After Will determines Holly's direction, he and Dad rush out through the jungle after her.

Holly reaches the Lost City, and her presence their is promptly detected by her brother. After some concentration, Will is able to realize that she has gone there to recharge the wand from the crystals. The Sleestak will be unable to harm her as long as she possesses (or is possessed by) the baton; no one should encounter any, since they are still asleep in hibernation. In the time doorway chamber, Holly saps the energy from huge crystals embedded in the walls, sending the pitch of the wand higher and higher. Its hum fluctuates wildly as she drains the crystals from the matrix table; the wand is now fully charged. Will and Dad arrive only seconds too late -- with the control table out of order, their chances of returning to Earth are severely damaged. Dad cautiously attempts to persuade his daughter to drop the flashing baton (which, by the way, suspiciously blinks in rhythm with her twitching finger), but too is zapped. Will rushes to his father's side, avoiding his possessed sister as she leaves the cavern, and once Dad composes himself, the men chase after her to the pylon.

Back in the jungle, Cha-Ka encounters Holly while returning to the Pakuni compound with a gourd of fresh water. "Aganza tusa" (magic big) he proclaims as he backs away in awe. Just then, Dad and Will arrive. Dad again tries to coax her into dropping the device, this time shielding himself with his backpack. Holly staggers toward him threatening him with the baton and drives him back. With one swift swing she knocks the pack from his hand; the blow causes him to fall. At the last minute, Will both saves his father and frees Holly from the evil charm by dousing her with Cha-Ka's gourd of water. After a moment of tears and comforting, Holly describes how she had to get back to the pylon. Will questions why the pylons no longer seem friendly; Dad reminds him that so far, they have merely been neutral. The children at first discourage their father from confronting the pylon, but they plead to stick with him when he stands firm on destroying it before it destroys them. He agrees when the kids remind him that they know where the pylon is located, and so avoiding the wand, they journey to subdue whatever power is responsible.

When they arrive, the pylon's doorway lies open. The Marshalls enter, gazing at the large green ball of light above the table. Will and Holly stiffen, and fail to respond their father's subsequent calls, so Dad begins removing the crystals from the matrix. Hauntingly, the controller of the pylon speaks through the children, demanding that Dad stop what he is doing. The being identifies himself as "the great and powerful, the watcher of the pylons, the possessor of the presence, the sleeper who has awakened", whose destiny is "to rule all". Dad boldly asserts that the possessor has no right to endanger and enslave other people; he continues to remove the crystals, defying the foe's command. In a desperate but fruitless attempt, the watcher makes the children plead sappily, but Dad, obviously wise to the con, keeps dismantling the matrix. As the last jewel is removed, the being gasps and dies, releasing Will and Holly where they drop to the ground. A brief moment of tears follows, after which the being's image comes into view. It appears to be an Altrusian, possibly the builder of the pylon. As the image fades, with their battle won, the Marshalls exit and make their way home.