The time gate to Zeal Kingdom has been sealed. You must find an alternate route.
Go Through Time to Return to Zeal
If you can beat Lavos now, do so to see the ending "What the Prophet Seeks"
Now fly on over to the Mystic Mountains and get to the gate at the top, to get to the End of Time.
First heal up with the sparkle near the save point, then use the pillar that takes you to Proto Dome.
Now you'll want to travel west through Lab 32 (if you want to avoid the monsters, race Johnny to get there... if you want an easier time of the race make sure boost mode is on).
If you want, you can travel through Lab 16 all the way to Bangor Dome and use the gate there. This opens the pillar to Guardia Forest 1000 A.D. at the End of Time. If you don't want to do this now, do it later.
From Lab 32, go straight down and into the dome at the base of the mountain.
This will be a piece of cake, because you were meant to go through the Sewer Access earlier in the game, the first time you reached the future. Your levels are way above the monsters in here.
Put Ayla and Robo in your party.
First, head down the ladder, and ignore the guard guy. Then head right. To avoid the monsters, walk north of them and at an angle down until you're to the right. Open the chest for cash. Avoid the monsters via the same route.
Now head left and fight the monsters (I don't think you can avoid them). Watch the scene, then go down and head down the ladder.
Head right. There's a diary to the left, it just says not to make a sound around here, or you'll be attacked. So, don't run, and don't touch ANY object in your path, NOT EVEN THE SAVE POINT. When you're past all the stuff, go up the ladder.
To avoid the monsters, hug the left wall. Go up past the bridge, then when you see a sort of a gap in the right wall, go through it. Hit the switch on the wall above, then go back through the passage.
Go up, then you can walk up behind the wall and go down through the door you opened with the switch. Watch the scene.
Continue on the path and open the chest. "Sir Krawlie" is next.
Just use physical attacks on this guy. He has an attack that takes your HP down to 1, so be sure to heal if he hits you with that.
Now hug the right wall and continue down, cross the bridge, hug the left wall and go down, cross the second bridge.
Go past the ladder first, open the chest, and flip the switch to form a bridge.
Then go back to that ladder and up. Go down to the dome below.
Head all the way to the top of the room, and open the sealed door. Check on each sparkle to continue on the path. Open the door at the end and go through.
Go all the way to the top of the room. Then, when you try to leave, the Nu comes in and tells you how to use this contraption. (When it falls asleep just try to move and it continues). (Default name: Epoch).
When that's done, check on the seats that the Nu pushed into the room to be raised into the machine.
Here's how it works:
Y - Time Gauge
+ - Select an era
A - Time travel to selected era
B - Quit
DON'T go to 1999 unless you want to fight Lavos right now.
Open the Sealed Chests
Now that you can go to any era at will, and now that you have the powered-up pendant, you have a way of unsealing those sealed doors and sealed chests, so it's time to hunt for treasure!
First, head to 600 A.D. and go into the Magic Cave which is right near where you land. Not too far into the cave is a sealed chest that holds a Magic Ring.
Now head south to Porre (if you see a swirling hole in the ground near Fiona's place, just ignore it) and visit the Elder's House. Check on BUT DON'T OPEN the two chests to the right. By checking on them without opening them, you cause the contents to be upgraded when you get them in 1000 A.D. Rest assured, you don't want to miss out on the upgraded stuff.
Note: You'll find some sealed chests in 600 A.D. that just open when you check them, meaning they aren't upgradeable.
Next go north to Guardia Forest. There's a sealed chest at the upper right of the forest that contains a Speed Tab.
Now go into Guardia Castle. Remember to leave normal chests alone in here. The sealed chest (just check, don't open) is up the stairway to the left of the King and Queen's thrones.
Finally go into the inn in Truce, to the east, and check but don't open the sealed chest.
Now head back to Epoch, and go to 1000 A.D.
Go south to Porre to the Mayor's Manor (formerly Elder's House), and open the two chests upstairs for the White Mail (absorbs lightning) and Black Mail (absorbs shadow).
Put Marle in your party and go into Guardia castle (listen to the Chancellor, what a jerk), then go up those stairs left of the throne. The sealed chest here contains the Red Mail (absorbs fire). You can also go around and get the normal chests here, the stuff is upgraded if you didn't touch them back in 600 A.D.
Now go to Truce Inn, the sealed chest is in the back, contains the Blue Mail (absorbs water).
Next, go to Lucca's house and talk to Taban for some new items. Then walk around the upper right of the island where Lucca's house is to find Vortex Pt. (there are a couple trees next to each other there). Use it to get to Heckran Cave.
Head down the stairs, all the way left, through the door below, and continue on the path (hugging the right wall if the Jinn Bottle is still there). The sealed chest is to the right, contains Wall Ring and Dash Ring.
Head back the way you came. Up the stairs from where you landed in the water when you got here, is the path out. You'll end up by Melchior's place.
Go through Medina Village and head for the forest to the north. Check on the pyramid to enter the Forest Ruins. Open the chest, then head up to find a weird pyramid. The pendant will open it, the Nu offers a Safe Helm or a Swallow (sword for Crono). The Swallow is not the best weapon for Crono so you may as well take the Safe Helm (the one on the left).
To make things easier on yourself, use the gate in the cupboard in the imps' house to get to the End of Time (otherwise you'd have to go all the way through Heckran Cave and find Epoch, which you'll do later).
At the End of Time, the old man may have something to say, so talk to him. Then use the pillar to Proto Dome.
Head through Lab 32, then go into Arris Dome. Go down the ladder and through the door to the right. Follow the path. When you can, go up the stairs behind the robot. When you're off that platform, head behind the robot and follow the path to a terminal that you can enter L&R&A on. Then open the sealed door and open the chests inside. There's also a Power Tab in the center of the room.
Now leave Arris Dome and go through Lab 16. Open the sealed door in Bangor Dome and open the chests. While you're here, use the gate in Bangor Dome. This will create a new pillar in the End of Time to Guardia Forest 1000 A.D. Use it, and get the sealed chest there. Then use the gate and pillar to get back to Bangor Dome.
Finally go to Trann Dome to the south and open the sealed door to get the chests and the Magic Tab to the left.
If you didn't get the Power Tab in Proto Dome before, you can use the gates and pillars to do it now. Once in Proto Dome, walk around in front of the gate until you hear a noise, and the Tab will appear.
Go back to the End of Time. Now that you've collected the upgraded Mails from the sealed chests, it's time to go back to 600 A.D. and collect the non-upgraded stuff since it's still there. So, make your way to Truce Inn, Guardia Castle (if you looted the normal chests in 1000 A.D. you can get the normal ones here in 600 A.D. though they don't hold very exciting stuff), and the Elder's House in Porre for the stuff. Then get back to the End of Time.
You've got everything from the sealed chests and stuff, so now go to Leene Square 1000 A.D. since Epoch is in that era. Find Epoch (near the mountain that used to lead to Magus' Castle), and go to 12,000 B.C.
The Skyway is locked now, so this time you'll want to go into the hut to the northwest.
Terra Cave & Algetty
In the first room of Algetty is a shop. Buy stuff there (but DON'T sell your Ruby Vests. If you have a Red Mail and Red Vest, you can sell all but one if you really have to).
There's an inn near the bottom of Algetty. Save down below.
If Ayla knows Charm, you can equip her with a Charm Top (accessory, not helm) and she can Charm R'Bow Helmets off of Beasts. If she's a long way away from learning Charm (for me she needed 200 skill pts), either go to the Hunting Range in 65 mil B.C. and fight Nus, or don't worry about it. I say leveling up for the helms is worth it.
In the bottom-right corner of the Beast's Nest, there is a Tab.
Go up and do away with the first couple of Beasts, then take the left path up. Kill the Beasts here, then switch your party to Crono, Lucca, and Marle.
Go up to start a fight.
Mud Imp, Red Beast, Blue Beast
Get to work on the Beasts. Ice Sword on Red Beast, Fire Sword on Blue Beast. It's best just to work on one Beast at a time. Once the Beasts are gone, use Ice Sword on the Mud Imp.