Chrono Trigger/Lost Sanctum

This is a small area (only available in the game's DS version) 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, too, 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 for 100,000 Gold

Prismastone
65,000,000 BC: 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 east. 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 east, 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 spent the entire time training to face 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 the easternmost Reptite to find out that you'll need some vines. They are found in the northeastern corner of the southern glade.

Go back to the broken ladder to trigger required dialogue. Then 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 needing 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. 65,000,000 BC:
 * Steel Ingot: Go to the southern glade and head west to find a cave. Find this in a chest in an alcove on the northwest side of the cave.
 * Hammer: Speak to the Golden Hammer guy to borrow it from him.
 * Godwood: Speak to the Reptite in the Millenia woods for some wood from the sapling's descendant.

600 AD: Speak to the builder and he'll give you a Haste helm before heading to the bridge. You cannot continue this quest until you complete the Lonely Soul quest. Return to the world map and re-enter the village. The neighbor will tell you that the builder never came back. Go up Mt. Emerald and speak to the Nu. It will move aside, allowing you to go on. Go through the cave (playing 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. Fight the enemies in the northeast corner (near the vines from the previous quest). After the battle, the Sweet Banana will be revealed.

600 AD: Bring the treat to the Nu. Construction will continue and the quest will end.

The Cave Conspiracy Quest
In Prehistory, talk to a Reptite near the bottom of the ladder that leads to the Northern Forest. It will tell you about how the Prismastone can be fused with another to form an even more powerful gem. Agree to show it to the Reptite. Go towards the twin ladders and climb to the village sanctuary. Place the Prismastone in one of the sockets and go to the Middle Ages.

600 AD: Go to the village sanctuary. It appears that the Reptite culture has changed in the past 65,000,600 years because the Elder refuses to allow entrance. He'll ponder over ancient tradition and say he'll allow entrance if you can retrieve a Reptmark. Just run up to the Northwestern point of the northern forest and press A over a glowing blue thing. See the Elder who'll step aside. Enter and grab the future Prismastone. Time for past and future to meet.

65,000,000 BC: Go to the sanctuary, and place the future Prismastone next to the current Prismastone. They'll fuse together and form the Saintstone. Get ready to trek up the mountain twice more! After talking to the Reptite who sent you on the time quest to begin with, take the Saintstone back to where you found the first Prismastone. Make sure to speak to one of the Reptite's neighbors about placing the Saintstone in a high area before you climb the mountain.

600 AD: Return to Mt. Emerald to receive the Waystone.

65,000,000 BC:Go back to the village. Talk to the Reptite in the Southeastern corner to find out about a dark cave. Agree to explore it. Go to the southern Swamp and go to the cave where you retrieved the steel ingot. Go to the western end and enter a door that appears bright. Enter to find total darkness despite the fact the door is lit up. The Waystone will shine, allowing entrance to the Primeval Fort. Enter to find out that it is inhabited by monsters who have an appetite for Reptite flesh or... scales.. or whatever. They'll spot you and attack. Kill them and proceed to the village (Automatically). After holding a meeting, your team will decide to vanquish more easy monsters. Go back to the Primeval Fort. Climb until you're in a room with two Chryosaurs running back and forth. There is a hidden door at the bottom. Enter and go through the hallway. You can then find a pair of chicken-legged Gargoyles that want a piece of you.

Back at the village, you'll be rewarded with a valor crest for you efforts.

Tower of Heavenly Idols Quest
600 AD: Return to check out the progress on the bridge. It's finished. You'll automatically return to the village, where you'll be awarded with Saurian Leathers. The Nu will set up a shop next to the Reptite that made it lunch. Try to go to the Southern Glade. You'll meet up with a Reptite who journeyed across the bridge. He says it leads to a tower with a creepy vibe to it. The Elder will ask you to check it out. Accept and climb the Mountain one last time. When you reach the tower, you'll run into a few more enemies, a Gaolor called a Deathguard, and a couple of bone knights. At the top, you'll run into the Reused Cyrus Ghost graphics called the Master-at-Arms, and his little Bladesman.

The Master-at-Arms is no more. Let's check on those idols. They're... you! Return to the village for the Championship Badge. (By the way, if you found a rusted blade in the tower, take it to the shop owner in the 65,000,000 BC Lost Sanctum for the Icewyrm, unless you already have the Rainbow) That concludes all the Reptite favors.