Jeremie does some investigating on the Internet about The Hermitage, and after a night of hacking, finds the deed to the house, signed by Franz Hopper. He also finds that there used to be a science teacher at Kadic with the same name, and wonders if they're the same person. Ulrich thinks it's likely, but Jeremie wants to be sure, and suggests checking Kadic's archives. Jeremie further suggests a connection between the Hermitage and the equipment in the Factory, and Lyoko too.
Aelita goes to the bathroom for a shower, only to find a long queue outside. It turns out that Sissi is occupying the bathroom and making everyone wait, which apparently happens a lot at Kadic. Sissi notices Aelita and tells her that with such a long queue, she might be waiting for a few hours, but adds that upstairs there are showers with no girls at all.
Aelita goes upstairs to the shower room, but it turns out that Sissi has played a cruel trick on her; it is the boys' shower room. Ulrich and Odd gently escort her out, and find Sissi, Herb, and Nicholas there, watching. Ulrich gets angry at Sissi for playing such a trick on Aelita, when she knows fully well that Aelita will easily fall for such things. Sissi doesn't appear to care. To make things worse, Jim tells Aelita off for trying to enter the boys' shower room.
Aelita meets Yumi and tells her about the recurring nightmares. Yumi assures her that it's just because she's not used to living on Earth; she's only been here for less than a week.
Jeremie sneaks into a room to check Kadic's archives, while Ulrich and Odd keep watch. He finds a document signed by the teacher Franz Hopper and compares the signature with the one on the deed to the Hermitage; they match, proving that they are the same person.
Jeremie, Odd, and Ulrich visit the Hermitage. Jeremie discovers a few history books on a shelf, including one about Carthage, which he knows a little about because they learned about it in school the previous year. Jeremie takes the book about Carthage.
At Kadic, Aelita is on her own in the cafeteria, trying to get lunch, but is unfamiliar with the workings of a cafeteria. Behind her, people waiting in line are getting impatient, and complain at her. She gets uncomfortable and gives up. For a moment she is relieved as she sees Yumi, but when she notices that Yumi is interested in a boy at her table, she gives up trying to get lunch and goes outside.
She meets Sissi outside the entrance, who starts being unkind to Aelita again, suggesting that she return up north. Aelita, distressed, tells Sissi that at least she'd feel at home there, and runs away into the trees.
In class, Mrs. Hertz notices that Aelita is not present, alerting Jeremie, Ulrich, and Odd to this too. Sissi tells them that Aelita has gone back to Canada, and recounts their last exchange. Jeremie pretends to be ill and asks to go to the Infirmary; Ulrich and Odd accompany him.
Jeremie quickly figures out exactly where Aelita must have gone; she has returned to Lyoko. They all race to the Factory with Yumi.
Jeremie sends Ulrich, Odd, and Yumi to Lyoko, where they find themselves under separate attack. They battle, trying to get to Aelita, but encounter heavy resistance. Jeremie sends them their Vehicles.
Unexpectedly, a white orb with the Eye of X.A.N.A. on it appears out of nowhere and engulfs Aelita. Jeremie loses touch with her; she has completely disappeared from his detectors. Yumi panics, fearing that Aelita has been killed by her attackers, but Jeremie thinks it isn't that. He finds that she has disappeared from the sector, and has actually disappeared completely from Lyoko.
Aelita leaves the orb, and finds herself in a blue, spherical room. An opening appears in the wall and she walks through it to explore, but is harrassed by slug-like monsters called Creepers. She encounters a huge monster with many tentacles - the Scyphozoa.
The remaining three on Lyoko continue to be attacked as Jeremie figures out what has happened. Jeremie discovers a fifth sector of Lyoko, one that they didn't know about before. It is named Carthage. Figuring that Aelita must be there, he tries to figure out how to get there, and finds he needs a code.
Ulrich tells Jeremie to hurry up, as the attack on Lyoko is getting fierce. Jeremie guesses that the code is related to the historical Carthage, and looks in the book he took from the Hermitage for words that might be the code. After trying many and failing, he thinks about it logically. He wants to get into Carthage, and to do that, he has to conquer it. He finds the name of the person who conquered Carthage, and enters it as the code: SCIPIO.
The white orb appears again on Lyoko, making the attackers back away. It engulfs Ulrich, Odd, and Yumi, and carries them through the forest at high speed, to a white void where many of the wires that run through the forest converge.
The orb travels through a dizzying arrangement of moving walls and arrives in what appears to be the same room Aelita arrived in. The three leave the orb and go to search for Aelita. They find her being attacked by the Scyphozoa, which Jeremie finds is stealing her memories. They attack it until it releases her.
The walls begin to close around them, and Jeremie tells them to hurry back. They return to where the orb dropped them off, and Jeremie calls another orb to return them to the Forest. Aelita enters a tower to devirtualize, while Jeremie materializes the other three directly from Lyoko.
Back on Earth, Aelita apologises for running away. The others comfort her, letting her know that they understand how difficult it is for her. Sissi comes to gloat, and Aelita surprises everyone by countering with an insult of her own.
- In the title of this episode, the word "Uncharted" is spelled incorrectly, and is spelled as "Unchartered".
- The original French name for this episode is Terre inconnue.
- This is the first episode to feature the Scyphozoa and the Creepers.
- This is the first time Sissi has been called by her real name, Elizabeth.
- First appearance of Carthage sector.
- First appearance of the Carthage Security Countdown.
- First appearance of Aelita's "memory count" scene.
- This episode was more risque in the original french script. In the scene in the showers, Odd would have slightly exposed himself to Sissi "out of frame", with some cursing. The scene was edited down.
- Uncharted Territory was released in Book form, but only in French.
- This episode introduces a plothole for all previous 27 episodes and the prequel. During those 29 episodes, X.A.N.A. has tried to destroy Aelita, however, starting with this episode, X.A.N.A. tries to prevent this at all costs since he need the keys of Lyoko to escape. But that would mean that, if X.A.N.A. would have managed to destroy Aelita, he would lose too.
- This could be because X.A.N.A. didn't have the power to make the Scyphozoa, and therefore believed that it had no way to get the keys.
- It could also be because X.A.N.A. was holding back in order to fool the Lyoko Warriors into boosting his own power using Time Reversion.
- Another explanation could be that X.A.N.A. had not gained enough power to be aware of the Keys to Lyoko's existence or that they held the power to allow it to escape the Supercomputer.
- By the standards of early 21st century computing, the code SCIPIO is insecure - passwords are recommended to be at least eight letters long, with numbers or punctuation in, and not to be known words.