This page explains how to do the Rainbow Shell sidequest.
Read The Fated Hour for instructions to get a Ruby Armor, which is helpful in this side-quest.
Start the Quest
First go to 1000 A.D. and fly to that little continent of Choras. Go to West Cape (NW area of Choras) and check behind the tombstone for a Speed Tab.
You CAN talk to Toma in 600 A.D. to learn more about this side-quest if you want to, but you don't have to.
Instead, go to 600 A.D. and fly to the island NW of where West Cape is going to be. Check on the front of the mountain to go in (if you talked to Toma then the mountain will be open and will be called Giant's Claw, but you can still go in either way).
If you haven't gone to 65 million B.C. and traded for the Ruby Armor, go and get one of those. Or, you can Charm one off a Gigasaur.
Equip two people with Lightning-absorbing armor.
Follow the path and read Toma's note if you want.
In the next room, you can sit in Azala's former throne and have a good laugh at the expense of the now-extinct Reptites. Continue down to the next room.
Head left and approach the chest to fight. Charm a Ruby Armor off the Gigasaur if you need one (you should only need one). On these guys, use Lightning, of course... but this time, the dinosaurs will sometimes zap you back with it, so watch out. When they're beat, open the chest (Sight Cap).
The door here leads nowhere, so head right. DON'T use lightning on the Lizardactyls. It actually heals them! Just use physical hits until they're gone. Then go right and through the door.
Step on the upper switch to create a save point, and use it to save. If you didn't open the chest beyond the skull so many millions of years ago, it's still there. Then hit the left switch. Don't step on the right switch or you'll have to fight. Fall into the hole (either side) to continue.
Leave the right switch alone, and step on the left. Go through the skull for a Tab. Exit the room.
There's a lot of treasure in this room. Continue until you see a ladder, and go down it. At the far right of this ledge is a Tab. At the far left is a chest (Full Ether). Go back up the ladder, and continue left. Stay along the outer wall to avoid fights. Before exiting the room, there's a chest behind an outcropping above the door (Blue Rock). Exit.
Continue, and go DOWN the ladder below you. The one leading up just leads to a one-way (i.e. broken) ladder and you'd have to go through previous rooms again to get back here. On this ledge go all the way left, past the slope down, and there's a concealed chest behind the rock wall containing a ZodiacCape. Now go down the slope and there's a chest to the right (Lapis). Then exit south.
You can avoid the next monsters by walking to the left of the left torch. If you approach each of them from behind they run away. Exit through the open skull (you'll see a Tab behind the other skull but you can't reach it... yet).
Step on the left switch to dispatch the monsters here, and go through the left door. Follow the path to a FrenzyBand. Then go back to the last room.
This fight is unavoidable, so fight and continue right, stepping on the switch and going through the right door.
There are Rubbles here, and you don't have to fight them, but as mentioned before, they give tons of experience. Continue to the next room.
Open the right-hand chest to fall below (it's the only way to continue).
Exit the cell and go up the left stairs. Get the Tab. You can go down and open the skull door and scare those Leapers again if you want. But don't go down the stairs on the left. You should head back the way you came, down the right-hand stairs.
Follow the path to the next room. A save point has magically appeared here. Use a Shelter and save. Then open Kino's former cell and go through the door that has appeared in the back.
Equip everyone with Fire-absorbing stuff, i.e. Red Mail, Red Vest, Ruby Armor. For this battle I used Crono, Ayla, and Robo.
Try walking past Rust Tyrano to start the battle. This guy doesn't do a "remove def, store pwr" like his ancient predecessor, so just attack away. Heal if anyone gets chewed up and spit out. Falcon Hit works fine, and Robo's Shock is good.
Go up to find... the Rainbow Shell! But it's too heavy to lift... so whoever's smartest in your party (it will be someone who actually talks, i.e. not Crono) will suggest enlisting the Knights of Guardia. After that, just leave, and watch the scenes that follow.
Now, put Marle in your party, and let's check out Guardia Castle, 1000 A.D.
If you didn't hear from the Chancellor when entering the castle with Marle, you will now.
The only way you can go (since all other paths are blocked by soldiers) is right from the entrance. Take the stairs up. Other paths lead nowhere interesting. On the way up, open the chest for a HyperEther. The other chest is locked. Hmmm...
Anyway, at the top of the stairs you reach the trial room, where if you talk to the guards, Marle will talk (shout) her way in.
Marle apparently doesn't remember getting the Rainbow Shell, even if she was part of the party that found the shell and talked to the King and Queen. Duh.
Now go back down the stairs, and when there's a separate stairway down, take it.
Walk towards the Gnashers, then kill them.
After the cut-scene, kill these enemies. Get the three reachable chests. Continue on. The Naga-ette here is avoidable.
Walk slowly up this hall to avoid a couple of Gnasher attacks. Then head up, get the three reachable chests, and make sure Marle is in your party (Lucca says something awesome if she's in the party too) and go up to the Rainbow Shell. Now that we have proof, let's hurry to the trial room.
But before you go... equip items on all your party members that protect status or protect against Chaos. For the upcoming fight I used Marle, Crono, and Robo.
Down this hallway you can just run to avoid fighitng. The Gnashers are too dumb to catch you.
In the next hallway you can avoid the Naga-ette as before.
Make your way up to the trial room, and talk to the guards who won't let you pass. Fortunately, Marle knows another way in...
DON'T use Lightning because he absorbs it. The main danger from this guy is his needle attacks. Just heal whenever he does these. For this battle I just used Super Volt.
Watch the scene.
Before you go to Melchior in the basement, go back into the trial room and get that sparkling thing (Yakra Key). Then head down the stairs and into the room with the locked chest. You can leave that chest locked, it just changes a game ending slightly. The Yakra Key unlocks the chest, and the real Chancellor is inside (just like 400 years ago).
Now go to the Rainbow Shell in the basement, and talk to Melchior to get new stuff (read below for details).
Here is some information about the PrismDress vs. the PrismHelms:
+ decrease damage from elemental spells by 1/3
+ ups defense by 99
- only get one
- can only be equipped by girls
- ups defense only by 40
+ get three of them
+ also ups Magic defense by 9
+ locks status
+ can be worn by anyone
It's a tough choice, but I lean towards getting the Helms. You can charm a Prism Dress later in the game.
Also, if you've done the Sun Stone side-quest, Melchior makes some even cooler stuff: Crono's best sword (Rainbow), and the PrismSpecs.
DON'T FORGET! If you didn't get it before, there are chests here in Guardia Castle 1000 A.D. that are ripe for the plucking. Go around and get them. Then go back and loot Guardia Castle 600 A.D., though the stuff there is (relatively) worthless.