I had a time travel plotline a while ago. Let's see if I can remember it properly. This was a homebrew world that used the default Grayhawk dieties from the PHB.
Sorry, this is kind of long. Probably longer than it needs to be, but I don't like to leave out details.
About 1000 years ago, there was a war that tore the Empire apart. The "bad guys" were led by somebody who wore the Eye of Vecna, and he wanted above all else to take over the Empire so he could have the resources to locate the Hand (ok, I know Vecna plots have been overdone, but work with me here).
Anyway, the war ends, the good guys win, butthe Empire is in shambles, and there's a nasty Eye of Vecna lying around. So the good guys build up a group of Heroes and send them off across the Western Ocean with the Eye on a quest to find a way to destroy or neutralize it.
And so the 7 heroes set off, led by a righteous Paladin.
Back on the mainland, these heroes were never heard from again.
Jump forward 1000 years.
The PCs have heard odd rumblings about a mysterious island that has suddenly appeared in the Western Ocean. Then they meet a medusa sorceress - who's had her eyes gouged out as punishment for attacking a temple of Hieroneous. She is desperate to see again, and convinced that the only thing that can reverse the curse of Hieroneous is the Eye of Vecna. The party, unable to defeat her in combat, agrees to find her the Eye. Of course, they're lying so that they can escape alive. But they correctly put together a couple clues I've dropped and assume that the mysterious island has something to do with the Eye.
They do a bit of research and find out about the 7 heroes and their quest 1000 years ago. They decide that they must have failed the quest. They decide that they are the ones who should go try to complete the quest, before somebody bad, like the Medusa, actually gets the Eye and uses it for evil.
So off they go on a ocean voyage that takes a session or two to complete. The details of the journey are not important.
So they arrive at the island, and the Druid does a quick scout in bird-form. It's basically a tall, extinct volcano, a few jungles, and a single small city on the coast. It's really a very small island. The people in the city are speaking some sort of archaic form of Common that the Druid can't understand.
So they dock at the port and cast a few Tongues spells and talk to the locals. Apparently, according to them, a few weeks ago a group of 7 adventurers arrived and spoke with the town elder. The elder was convinced that these 7 people matched the ancient prophecy stating that they should be given the Time Jewel, for the good of mankind. The Time Jewel is, apparently, a powerful artifact with powers to manipulate time. Without further ado, the 7 people (matching the description of the heroes from 1000 years ago) set off for the extinct volcano.
(You see where this is heading yet?
)
They ask a few questions about the volcano. Apparently, several hundred years ago (according to the locals), a powerful Lich named Vecna lived in a complex there, feeding on the powerful "Magic Node" that surfaces there. When he ascended to godhood, he left the place abandoned. Any magical item or effect within range of the Node is intensified exponentially.
The party correctly assumes that the Heroes intended to use this Node, in conjunction with the Time Jewel, to neutralize the Eye of Vecna in some way. But what went wrong? The city dwellers remember the heroes arriving mere weeks ago.
And there are further complications, just becuase I'm an aspiring Rat Bastard that way.
Shortly after the heroes should have arrived at the abandoned Vecna-complex, everybody in the town started aging rapidly. At the rate of one YEAR every other day. Remember, it's been weeks now, and everybody has aged 15 years during that time. The town guard is seriously weakened by this, the elderly have all died from old age, and things generally suck. (this effect is caused by the poorly managed time travel that threw these people 1000 years into the future. Their bodies are aging rapidly to catch up.)
That's not the only complication.
Right after the aging started, the city started to get raided at night. First by a handful of undead, each killing one person and hauling away their body. Then then next night, the stolen bodies were animated and following the same program. Kill one person, steal the body. This is leading to exponential undead-population growth. The undead are of a type never seen before (JuJu Zombie template) and the city dwellers have had no luck trying to kill them (damage reduction).
The PCs correctly assume that the heroes were zombified, and started the chain of exponential zombification. They now have multiple reasons to go to the extinct volcano and investigate the complex.
They travel up to the entrance (inside the volcano rim) and reason (correctly) that if they wait for the zombies to come out at night, there will be fewer monsters for them to deal with inside.
Once inside, they find some of the more nefarious puzzles I've ever concocted. Plus they're on a time limit - they have to finish before the zombies come back - so they can't rest. Eventually, they win their way through to the final chamber where the magic of the Node is at full force. They defeat the JuJu zombie incarnations of the Heroes, and find the weeks-old body of the righteous paladin who led them (not zombified).
They find the journal of one of the Heroes. It describes, in horrifying detail, how the Quest progressed. The paladin was immune to the corruption of the Eye, but the other Heroes were not. Slowly, it drove them mad. They belived the paladin was going to use the Time Jewel and Eye in some sort of evil ritual, and concocted a plan to ruin the ritual so that it wouldn't come to pass. When they did so, the power of Vecna's old altar (upon which they were foolishly conducting the ritual) was activated, and the whole lot of them were zombified. Except the paladin, who is apparently immune to that kind of thing.
This disruption also released the power of the Time Jewel in a horrible way, amplified by the power of the Node. The entire island was then thrust forward in time 1000 years. The original plan of the ritual was, according to the journal, to seal the Eye away in a "pocket" of time where it would never be accessable to the world again. The amplification of the Node would make this pocket permenant.
The Eye is still clutched in a death-grip in the dead paladin's hand.
The PCs figure out what they need to do to complete the ritual.
*poof!* the Eye and Jewel vanish, sealed away forever.
*poof!* the room around them shimmers and ages.
The PCs find themselves surrounded by people. Civilians of some sort.
A man approaches them and proclaims the prophecy has been fulfilled, the thousand year banishment is at an end.
It becomes clear to the PCs that when they sealed away the Jewel, the island and its occupants were sent back in time 1000 years, and to them time has progressed normally since then. The PCs, not being part of the time accident, stayed put. To the PCs, the island has just aged 1000 years in an instant while they stood still. They are legandary heroes to the islanders, who saved their ancesters from certain death 1000 years ago.
Meanwhile, for those 1000 years, the island has been sealed off in an impenitrable mist that is apparently the universes' way of preventing paradox. Nobody could get in, nobody could get out, until the "loop" of time worked out its kinks. I.e., the present time was reached.
This mist cut the island off from weather systems, currents, etc... The island is now a sandy desert occupied by a colony of blue dragons. The villagers have taken refuge inside - and lived for centuries within - Vecna's complex. Their prophecies say that 1000 years after saving their lives, the heroes will appear again, just as they were 1000 years ago, and save them from the dragons.
And that's pretty much the end of the time travel stuff. The players congratulated me on a tricky way to get them on an island surrounded by dragons and having to find a way out. It WAS pretty sneaky, if I do say so myself.