The Lost Sanctum has many locations within it that can be traversed on foot.
The Lost Sanctum consists of two dungeons and a village of Reptites. You perform quests for the villagers in the two different time periods to receive special rewards.
Clear the Forest
Once Crono's party arrives in the prehistoric Lost Sanctum, they find the entire village deserted. After looking around a bit, the party goes off into the forest to the north and clear it of monsters. Once they return, the Reptites inhabiting the village come out and reward the party with a Dragon Tear. After clearing the forest in 65,000,000 B.C., the party can now enter the 600 A.D. Lost Sanctum, which had previously been overrun by monsters. Once the elder determines that the party members are the "heroes of legend" passed down in their tradition, and are once again employed to clear the Millennia Wood of monsters. The Reptites will yield a Megalixir when completed.
The Golden Hammer
Once the party clears the woods of monsters in Prehistory, a Reptite in the lower left part of the village requests the party to find the legendary "Golden Hammer." Another Reptite gives the party a hint that sprinkling a sapling with Golden Sand will cause it to become a golden tree. The party departs to the Great Southern Swamp to find some of the sand. After retrieving the Golden Sand, the party, as instructed, sprinkles it on a sapling at the end of the Millennia Wood. The party then departs for the Middle Ages to find the grown golden tree, but instead, they find Goldhammer, an Ogan that presumably chopped down the tree and already made a Golden Hammer. The party goes on to defeat it and it surrenders the hammer, which is then given to the Reptite in prehistory for a reward.
Returning to Prehistory, the party receives a new quest from a Reptite in the upper left. Her daughter has fallen ill and needs the restorative qualities of the "Prismastone" to be cured. However, in order to procure the said item, the party needs to traverse Mount Emerald, which is guarded by the Nu Guardian, a dark-colored Nu that blocks the way at the base of the peak. After defeating the Nu, the party makes their way to the summit, where they find the Prismastone, which is taken back to the girl's mother for 2 Strength Capsules, 2 Magic Capsules, and 2 Speed Capsules.
After the above quest is complete, a gem collector in 65,000,000 BC (the upper-right Reptite) wants to be shown the Prismastone the party just collected. After offering it to her, she will request to see the "Saintstone," a gem that can be created by the merging of two Prismastones. The party then places the Prismastone on the altar in the Reptites' shrine. Once in the Middle Ages, the elder does not permit the party to enter the shrine unless they bear the Reptmark, which the party procures in the woods to the north. After removing the 600 A.D. Prismastone, the party uses the Epoch to return to Prehistory to merge the two Prismastones into the Saintstone, and is shown to the gem collector for a Dragon Arm for Robo.
Befriending the Nu Master
Now in the Middle Ages, the party comes across a Reptite (where the Reptite that requested the Golden Hammer was in the past) that tells them of a strange character that has been seen at the foot of Mount Emerald. This character has been waiting for a "strong person" all alone for thousands of years. The Reptite thinks that he must be lonely, and asks the party that they check on him. Agreeing to do so, the party travels to Mount Emerald to discover that this figure is none other than the Nu Guardian they defeated 65,000,600 years in the past, who has honed his skills and become the Nu Master. The Nu Master challenges them to a rematch and beckons them to the summit of the mountain, where he will be waiting. Unfortunately, over the many years, the ladder that leads to the path to the summit has broken, leaving the party to make a new one. A Reptite in the village hints that sturdy vines that can make a ladder can be found in the Southern Glade. The party is able to find some, but they are unable to make the new ladder in that period in time. Returning to Prehistory, the party reaches the necessary point in Mount Emerald and make the ladder there, where it will replace the one that will eventually break down in the future. Back in the Middle Ages, the new ladder has remained, and thus the party is able to proceed to the summit. At the top, they are greeted by the Nu Master, who engages them in battle. Despite his hard work and training, however, he is still bested by the heroes. They then tell him that strength isn't everything, and maybe he should try to be friends with people, too. The Nu Master considers this and asks the party to be his friends, telling them that he will help them if they need something of him. With that, the party goes back to the Reptite village and informs the Reptite that they obtained the Nu Master's friendship, and are given the Nova Armor as a reward.
Building the Bridge
still, in the Middle Ages era, the Reptite next to the ladder leading to the Millennia Wood tells the party of his dream to build a great bridge that spans the mountains but has been unable to do so. He asks them to find lumber, metal, and a hammer to him so that he has the materials to build this bridge. For this, the party must obtain the Godwood, which they are told by a Reptite in Prehistory they can get from a Reptite in the Millennia Wood, and the Steel Ingot, which they are told it is found in the Winding Passage at the end of the Southern Glade in the Middle Ages. In addition, they must also borrow the Golden Hammer they had previously obtained and given to a Reptite. With these three materials in hand, the party must talk to the bridge builder and give them to him. Now that he can build his bridge, the builder gives the party the Haste Helm as a reward and leaves to the mountains.
Finding the Bridge Builder
Later, after the bridge builder has gone, his neighbor will tell the party that he hasn't been coming home late. They are asked to go look for him in Mount Emerald, where he is building the bridge. At the summit, the party asks the Nu Master if he has seen the bridge builder, who tells them that he is right there in the summit, past a small cave. The party ends up finding the builder, who it turns out has fallen and is hanging on to the bridge for dear life. The party pulls him back up, and the builder gives his thanks. He then asks them to find a strong, durable person that can help him finish the bridge. The party then asks the Nu Master for his assistance, for which he agrees willingly. The two start working farther on the bridge, but the Nu Master starts getting hungry, and can't move until he has food. Back at the Reptite village, the Reptite who first asked the party to help the Nu Master offers a Hearty Lunch to take to him. After giving it to the Nu Master back at the bridge site, he feels better to work again, but he once again asks for food; specifically, a "sweet yellow thing" that monsters used to have a long time ago. The party tries looking for this food in Prehistory, and they find, along some other things, a Sweet Banana, found dropped by a Deathcreeper in the Great Southern Swamp. The party returns to Mount Emerald in the Middle Ages and gives the Sweet Banana to the Nu Master, who takes it gladly and proceeds to finish the Great Bridge. The bridge builder remarks it's almost done, and that the party should wait for a little while.
The Dark Cavern
For this quest, the party attempts exploring the Winding Passage in Prehistory, but find that at the end of it is a pitch-black cavern, as they were told by a Reptite before, making it impossible to proceed forward. Another Reptite tells them that the Prismastone absorbs light, and if they were to find a similar stone, they could place it on top of a peak for thousands of years so that it'd shine bright as the sun. With this information, the party goes to the peak of Mount Emerald and places the Saintstone there. Going forward to the Middle Ages, the party returns to find that over the millennia the Saintstone has absorbed a great deal of light and has become the brilliant Waystone. With it in hand, the party goes back to the Reptite in Prehistory who told them of the dark passage and agree to explore it on his behalf. The Waystone completely brightens up the Lightless Cave, and so the party is able to proceed. They come across a strange fortress, and they are able to overhear a group of Twin Snakes that reveal that they along with their boss are planning to eat all the Reptites in the village. The snakes catch the party, but they are fought off, and the party races back to the village to warn them. The villagers prepare to flee, but when the party offers to help, they decide to accept their help and give them the Judgement Scythe to help them on their quest.
Defend the Village
The party thus ventures back to the Primeval Fortress, finding that the invaders have already gotten as far as to the entrance of the Winding Passage, and defeat them before they get any further. Inside the fortress, they find a stronghold quite similar to the Tyranno Lair in technology and architecture, as well as the creatures that inhabit it. At the end of it, the party finds the elder Archaeofang and the younger Archaeofang, the two brothers who rule the Primeval Fortress and are planning the assault on the Reptites. Though the beasts were formidable, having even the ability to revive each other, they were defeated by the heroes, thus saving the Reptites. The village is eternally grateful to them, and reward them with the Valor Crest.
Tower of the Ancients
Once the Primeval Fortress has been cleared, the party can return to the Great Bridge in the Middle Ages to see that it has been completed at last. Everyone returns to the village, including the Nu Master, who has decided to stay in the village in the company of the Reptites. The bridge builder rewards the party with the Saurian Leathers for their hard work. Afterward, a Reptite comes running from the mountains, saying he has seen a huge, eerie tower across the new bridge. The elder of the village then reveals that this tower may be the tower spoken of in legends, where the Heavenly Idols of the village rest. He asks the party that they go to investigate it and see what is so eerie and gloomy about it. Inside the Tower of the Ancients, the heroes fight their way to the top, encountering the Master-at-Arms and the Bladesman, the source of the evil apparitions in the tower. The party defeats them, and so they go look for the Heavenly Idols. Once they are found, the party is shocked to find that the idols are actually statues of themselves, the heroes who first arrived in the Reptite village and saved it from monsters 65,000,000 years ago. The party then returns to the village, telling the Reptites that the tower has been cleared of the evil spirits besieging it. The villagers decide to thank the heroes with the treasure that is dedicated to their greatest champions, the Champion's Badge, ending every important event that can happen in the Lost Sanctum.