The Ark is dispatched to check on a village where the young somehow rule the old.
Young Diana walks along a dirt road, calling for her grandfather. He comes out of hiding, asking if she's alone. He's suspicious of her, wonder if she's really the one talking. Three men appear at the top of the hill and begin chasing the old man. He expresses disappointment at her betrayal then tries to run, but trips as he reaches another road. The old man strikes his head, falling unconscious. The young girl only watches with no emotion.
The Ark comes upon the man sprawled on the ground as they approach the village. Jonah brakes hard then exits through the front steps to check on the man. The other Ark crew follow while the pursuers return to the village. Inside the Ark, the man mutters something about his granddaughter being in danger before losing consciousness again. Jonah takes the Jet Jumper to investigate the village. As Ruth tends to the man, Samuel detects strange sounds. He notices they're alpha waves just before he becomes mesmerized.
Jonah lands on a small wooden bridge, where he finds Diana. He tells Diana that her grandfather's been hurt. She says Omega can help him and offers to take Jonah to Omega. Jonah calls the Ark, snapping Samuel from his trance. Ruth tells him that the old man will be okay. As Jonah signs off, Samuel begins hearing sounds again, then a deep, reverberating voice. It beckons to him and he activates the Roamer. Ruth can't hear the sounds or the voice and is unaffected. She can't stop Samuel so she has Adam jump into the Roamer to keep an eye on him.
In the village, Jonah sees the older people doing all of the menial labor. When he asks why, he hears the same voice Samuel did, offering answers. Jonah follows the voice to a black obelisk with three white squares on its face, surrounded by a small pool and a grid of white squares. Jonah recognizes it as a computer. It explains that it is solving problems by controlling the young and repressing the older people, the ones who caused civilization to fall. Omega tries to control Jonah's mind but fails. The younger minds are easier and quicker to control. Omega boasts that Samuel is already coming to join it. Jonah tries to call the Ark, but Omega has jammed his communicator. He decides to try to shut off Omega. Before he steps on the grid, Omega issues a warning that its defense mechanisms have been activated. When Jonah throws a stick over the grid, a laser shoots straight up, blasting it into a smoking cinder. Jonah takes off to return to the Ark as the Roamer enters the village.
Jonah arrives at the Ark, where an alarmed Ruth tells him about Samuel's abrupt departure. Jonah tries to call Samuel, but receives no answer. Samuel stands before the obelisk, where Omega welcomes him. Adam pleads for Samuel to go home, but Samuel doesn't seem to hear him.
Diana's grandfather explains to Jonah how Omega came to be. It was built by a society that no longer exists. Three weeks previous, the village decided to reactivate Omega, thinking it could help them. It quickly took over the village, starting with the youngest, most pliable minds. The grandfather, being the oldest in the village, was slowest to be affected and ran when he saw what it was doing. Ruth's research has revealed what the computer is, a Checkmate system, model Omega, built in the 21st century. Jonah is excited that they can deactivate it, until Ruth reveals that getting through the checkerboard grid takes a precise sequence of moves through it. They begin feeling Omega's influence again. The grandfather advises they get out of Omega's range while they still can. Jonah refuses to leave Samuel behind.
Jonah flies back to Omega, where Adam's presence has puzzled the machine, since its data says chimpanzees can't talk. They're using new anti-scrambling technology so Omega won't be able to interfere. With Ruth transmitting the instructions, Jonah begins hopping from square to square on the laser field, occasionally being almost too late when lasers erupt beneath him. Omega continues to transmit, weakening their minds. Jonah makes it through the field but must push buttons in each of the three squares on the face of the obelisk. Omega is alarmed when Jonah pushes the lowest button. It orders Samuel to stop Jonah. Samuel pulls Jonah's arm away from the obelisk. Jonah beseeches Samuel to help him. Samuel resists Omega and stiffly pushes Jonah's arm back up to reach the second button. But he can't reach the final, highest button. Adam jumps onto his shoulders and, with Jonah and Samuel's help, pushes the button. Omega shuts down as young and old villagers reconcile. Jonah wants Omega reprogrammed, but pushing the buttons has already done that. It will now serve instead of command. The Ark arrives, reuniting the guilt-ridden Diana and her forgiving grandfather.
Ruth drives the Ark to their next mission while Jonah makes his log entry that young and old need to work together to survive.