Chrono Trigger/Lost Sanctum

This is a small area accessible in 65,000,000 BC and 600 AD. It is located at a northern point near Ozzie's fort in 600 AD, and near the Sun Shrine in 65,000,000 BC.

65,000,000 BC
If you go to the Lost Sanctum during 600 AD, you'll find it overrun with monsters. To get around this, simply go there during 65,000,000 BC and you'll find that same cave deserted. Head northeast and exit the cave to a northern forest. You'll spot a group of monsters there, and your team will decide to vanquish them. If you look at the map on the bottom screen, you'll find the little hidden areas easily enough. After you've vanquished all the monsters, head south to the cave and you'll find a reptite. Apparently, they weren't all killed by Lavos after all. You'll learn that the Reptites have been struggling to survive against those very same monsters and that you've given them freedom. You can agree to do various missions for the Reptites for a compensation of some kind.

600 AD
Head north from Ozzie's fort to find the Lost Sanctum. Upon entrance, you'll see that the monsters that were there before are now gone. As an added bonus, the Reptites of this period are giving reward missions to your "Legendary Heroes (Or simply hairless apes)". Your first mission is to go clear that same forest of monsters. Mostly, you'll face Imps. New treasures have popped up to, so look into those. Afterwards, talk to the Reptite elder for a Megalixir.

Golden Hammer Quest
65,000,000 BC: Start this quest by talking to a guy in the southwest corner. Apparently he needs a special Golden Hammer for some reason or another. Agree to help and enter the southern swamp and look around for a key item called the Golden Sand. Go to the Northern Woods (hence called Millenia woods) and go to the area where you vanquished the last of the monsters. You'll come across a tiny sapling. Press over it to sprinkle the sand over the sapling and get this party started.

600 AD: Return to the Millennia woods and return to the spot where you planted the Golden Tree. You'll find out that some Ogan decided to chop it down. The Ogan will run off into the woods, but it couldn't have gone far. Chase it until you engage into battle.

After you've beaten him, he'll give up the Golden Hammer.

65,000,000 BC: Return to the Reptite and hand over the hammer.

Prismastone
600 AD: Head to the Northwest to find a Reptite who has a sick daughter. She needs to heal her daughter with a legendary prismastone that can only be found on a mountain to the west. She can't go because a "fearsome guardian" is blocking the path up the mountain. Agree to help and head south to the swamp. Go all the way to the bottom, go west, and head north to enter a new map. You should see a blue Nu sitting on the path up. Maybe he knows where the guardian is. Speak with the Nu to find out that he's the guardian. He says that if you beat him, you can proceed. Accept his challenge. Boss battle!

Continue up the mountain and you'll arrive at a little ledge with a jewel thing. That is the Prismastone. Take the Prismastone back to the village and give it to the Reptite. Her daughter is healed in full and you're rewarded.

Lonely Soul Quest
600 AD: Speak to the guy who lives where the Golden Hammer guy lived 65,000,600 years ago to find out that the Nu has be waiting for a strong person to show up and fight. Agree to check into it and go to the Southern swamp. A lot's changed in 65,000,600 years. Move through the southern glade and head to Mt. Emerald. Speak to the Nu, which turned itself black. Apparently it's spent the entire time training for you. It will head up the mountain awaiting your challenge. Try to head up and you'll find out that the ladder is out. Head back to the village and speak to a northeastern Reptite to find out that it likes to build. It needs some materials. You'll find some vines in the northern part of the southern glade. Go back to prehistory and hang the ladder on the mountain. Return in the Middle Ages and climb to face the Nu.

After you've finished off the Nu, He'll become your friend. If you need something from this Nu, which we may be needed in the future. Talk to the Reptite for a Nova Armor.

Bridgebuilder Quest
600 AD: A builder wants to fix a bridge on the mountain. Here are the materials and their locations:
 * Steel Ingot: Go to the southern glade and head east find a cave. Find this in a chest.
 * Hammer: Speak to the Golden Hammer guy to borrow it from him.
 * Godwood: Speak to the Reptite in the Millenia woods in 65,000,000 BC for some wood from the sapling's descendant.

Speak to the builder and he'll leave for the bridge but never come back. Speak to his neighbor to activate the quest. Go up mount. Emerald and speak to the Nu. It will move aside, allowing you to go on. Go through the cave with the Ocean Palace music, and you'll see that the Reptite is hanging on to the bridge by his teeth. After you pull him up, he says he needs some help fixing the bridge. Run to the Nu and he'll be delighted to help. Part way through, the Nu will run out of energy and need to be fed. Go to the village and talk to the guy who sent you on the lonely soul quest. He'll give you a hearty meal, which is just what the Nu needs. Bring it to the Nu and he'll enjoy it. He'll think back to the good ol' days when he had some kind of yellow treat.

65,000,000 BC: Go to southern swamp and find a Sweet Banana. When you do, return to the Nu.

600 AD: The bridge will be finished, and the quest will end.