Break the Seal! (2300 A.D. second time and 12,000 B.C. second time)
Backtracking and Sealed Chests
Items: White Mail, Black Mail, Red Mail, Blue Mail, Epoch, Power Ring, Wall Ring, Dash Ring, Taban Suit, Speed Tab, Magic Ring, Swallow/Safe Helm, White Vest, Black Vest, Red Vest, Blue Vest, Power Tab, Lumin Robe, Elixir, Hit Ring, Gold Erng, Charm Top, Full Ether, Wallet, Magic Tab, Gold Stud, Full Ether
Head back to the end of time and you'll discover you no longer have all 9 time portals open. Bummer, huh? Talk to Gaspar and he'll hint at a man who was building a time machine. To find him you'll need to go to the keeper dome in the future, but you might want to do a few things first. For starters, now that you have a charged up pendant you might as well backtrack through 600 A.D., 1000 A.D., and 2300 A.D. for all sealed doors and chests you've found before but have been unable to reach. You won't be able to get to all of the places where they're hidden now, but check the section on Sealed Chests for more info, I'd highly recommend picking up these items before the next section.
Also, the route to Guardia forest will be blocked off now to make it more difficult to access that sealed chest, if you haven't done so already, you'll want to backtrack through 2300 A.D. and access the time gate between the Bangor Dome and Guardia Forest. The Cathedral in 600 A.D. will finally have an actual nun show up in it. One more thing is that if you're really ambitious you may be able to do the Sunken Desert sidequest at this point in the game, provided you told the girl to secretly plant the sapling already. This area will provide an extremely excellent place to grind, as you will gain a lot of XP and TP while having a place to rest at all times.
The Keeper's Dome
Items: Epoch, Magic Tab
One side note since you'll be going to the future anyway, is that you can go to the Arris Dome and the Trann Dome to talk to the people there, who will be starting to plant seeds and rebuild their lives. Anyway, warp in to either the Bangor Dome or the Proto Dome and cross through Lab 16 on foot or Lab 32 on foot or the jetbike to get to where the sewers are. If you haven't already cleared it out, check out Beyond the Ruins for more info. It's a really easy area, and if you've already beaten it you should be able to walk across the bridges you activated to the Keeper's dome.
Talk to the Nu if you like, then head through the sealed doors to read Belthasar's recorded messages. Head through the next sealed door, go to the back of the machine and interact with it. Try to leave the room and the Nu (Belthasar's memory) will enter with the seats of the cockpit. You'll gain his "Wings of Time" and get a chance to name it. Take off with it to see what it's capable of, and you'll be able to head back in time to 12000 B.C.
One thing you might want to do before take-off is return to the room where Belthasar left all of his messages to find a Magic Tab. Gaspar will also comment on it if you visit him at the end of time.
12000 B.C. revisited
Enemies: Beast, Mud Imp, Red Beast, Blue Beast
Items: Power Tab
Purchasables: Demon Edge, CometArrow, Megablast, MegatonArm, FlashBlade, Lumin Robe, Flash Mail, Glow Helm, Tonic, Mid Tonic, Full Tonic, Heal, Revive, Shelter, Ether
If you wander around you'll soon find out that the skyway has been sealed, tough luck. Head to the northwest to check out the Terra Cave and talk to the "Earthbound Ones." The one living on the top level offers the best armor and weapons available in the game so far, although you might find it impossible to afford all of them, choose some for the characters you'll want to use.
He sells Lumin Robes for the girls and Flash Mail for the guys/frogs/robots. Note that of the items available for sale, the weapons (with the exception of the Demon Edge) will not be available for sale after the Ocean Palace (the Demon Edge as well as the of the armor can be bought in Medina Village for either high or low prices, depending on whether the Ozzie's Fort quest has been completed). Head to the bottom, save if you like, and head into the next area, making sure to pick up the Power Tab in the bottom right corner. You'll fight two pairs of beasts (separate fights), a boss battle. Charm at last 6 RainbowHelm off those Beasts for your party, its the best Helm up until now (even better than Glow Helm which you could buy earlier).
After you beat the trio, you'll officially be in the next chapter.
If you go back and challenge Lavos at this point, you should get The Prophet Ending. There will be a few scenes involving "the Prophet" from this period and a particularly nice speech from him, hinting that he would have gotten the chance to do what he wanted without your interference.