While travelling in a shuttle to the planet Ledos for a conference on Warp Field Dynamics, Chakotay and Seven of Nine take a detour to admire the natural landscape of one of the planet's subcontinents, and in doing so they scrape a mysterious energy barrier that starts to break the shuttle apart. Seven uses phasers to open a rift in the barrier, and they beam to the surface before the shuttle explodes. They find themselves stranded in a lush jungle, and in spite of Chakotay's leg injury, set out to find the shuttle debris in hopes of constructing a beacon to send a distress signal.
Meanwhile Tom Paris flies the Delta Flyer somewhat recklessly through the bustling Ledosian spaceport, and learns from the Port Authority that he has committed a piloting violation. Captain Janeway later informs Paris that his penalty, under local law, is to take a three-day course in flight safety, and since she has decided to grant the crew shore leave on the planet, he'll have time to complete it — much to his chagrin.
On the surface, Chakotay and Seven discover a tribe of primitive humanoids living in the jungle. Agreeing they should avoid contact with them, Chakotay — who is developing an infection — rests while Seven continues searching for debris. While she's away, three native men sneak up on Chakotay. Just then Seven finds a working piece of the shuttle and summons Chakotay, and the natives, startled by her disembodied voice, grab his combadge and destroy it. Seven returns and finds that Chakotay has been taken into a cave. It turns out the natives are friendly, and they are treating his wound. Chakotay talks Seven into staying the night, but she is uncomfortable with the degree of fascination the unspeaking natives have for them, especially an adolescent girl who is intrigued by her Borg implants.
As Harry Kim, Neelix and B'Elanna Torres prepare to beam down to the planet for shore leave, they tease Paris for having to attend "pilot school." Paris is confident he can skip right to the test and join them in a couple of hours, but then the flying instructor, Mr. Kleg, beams aboard and makes it clear he intends to take as much time with Paris as he deems necessary.
The next morning, Chakotay begins to learn the natives' sign language as he draws a map in the ground to get his bearings. Seven tells him she can construct a beacon by connecting the components she found with the shuttle's deflector, which she has detected six kilometers away. Since he's still injured, Chakotay suggests letting one of the locals guide her, but she won't because she's still trying to limit contact with them. As she makes her way through the dense jungle brush, she takes a fall and loses her tricorders into a crevice, and has to proceed without it. Meanwhile, Chakotay makes a startling discovery: the native men have started painting tattoos on their foreheads that look like his.
That night, Seven has to endure cold and rain, but then the adolescent girl shows up and brings her a blanket. The girl builds a fire and offers Seven food, which she turns down. The next morning Seven finally accepts the food, and allows the girl to guide her through the jungle. Along the way, though, the girl insists they stop and admire the view of spectacular triple waterfall. Back at the encampment, Chakotay is worried about Seven, and when he tries to communicate that he needs help to find his friend, a native man misunderstands him and brings out a woman who has strapped a small piece of shuttle debris to her forehead, to emulate Seven. Chakotay finds out they have retrieved several pieces of technology from the shuttle, and gets them to lead him to where they found it. Meanwhile, Seven and the girl find the shuttle deflector.
On Voyager, Tuvok reports to Janeway that Chakotay and Seven have failed to report in, and they never showed up at the conference. Tuvok and Kim have located a wing from their shuttle resting on top of the energy barrier surrounding the southern subcontinent, which means the missing crewmen are probably there, but they cannot be sure because the barrier is deflecting all their scans. Janeway contacts the Ledosian Ambassador, who informs her that the barrier shields the territory of the indigenous Ventu, and it was erected centuries ago by aliens to protect the Ventu from having their culture destroyed by the Ledosians' own unenlightened ancestors. But the technology is a mystery to them, so they can't lower the barrier, and since it's generated from the inside, the Ambassador holds no hope that the crewman, if alive, can ever get out.
On the surface, Chakotay meets up with Seven, and they recruit help from the Ventu men to move the deflector to a spot where Seven believes she can generate a deflector beam to temporarily neutralize the barrier, thus allowing them to escape and Voyager to beam away all their technology. Meanwhile Voyager is attempting to penetrate the energy barrier with phasers, but feedback from the barrier is interfering with the ship's systems, forcing them to cease. A short time later, though, the crew learns the barrier is being deactivated from the inside. Seven has successfully generated a dampening field, but the Ventu girl gets too close to the deflector and receives a serious shock. When Janeway's voice comes through telling the crewmen to stand by for transport, Seven reports that she needs to remain behind to treat an injury.
After the Ventu girl recovers, Seven says goodbye and accepts the girl's blanket as a gift. Just then she hears voices approaching — a Ledosian expedition has arrived to conduct scans and evaluate the habitat for development. Barus, the expedition leader, tells Seven she did the Ventu a great favor by lowering the barrier, because now they can benefit from education and technology. On board Voyager, Seven, Chakotay and Janeway debate whether or not the Ventu would be better off losing their isolation, but decide their unique way of life is worth preserving. When Janeway announces to the Ledosian Ambassador her intention to restore the barrier, he protests, but says he will remove his people from the territory. However, when Voyager tries to beam up the deflector assembly, a Ledosian vessel fires and knocks out their transporters. Janeway then contacts Paris, who is still in the Delta Flyer maneuvering through a training course with Mr. Kleg, and gives him encrypted orders. Over Kleg's objections, Paris suddenly peels away from the course and rushes to the planet. He beams up the expedition team, then finds the deflector and vaporizes it with phaser fire, and zooms away a split second before the energy barrier goes back up. Mr. Kleg tells Paris he has failed the course.
Back on board, Seven tells Chakotay she's concerned that the Ledosians may have scanned her deflector modifications and could find a way to remove the barrier themselves. She realizes if she hadn't made those modifications, the Ventu would be safe, but they would still be stranded. All she and Chakotay are sure of is that they're glad to be back on Voyager.