Ok, I have most of it written. Here is how it goes down.
At the end of the last play session, MOST of the characters were on a Goblin airship with a punctured balloon that was heading AWAY from the Battle of Otterville. A few characters were on the ground fighting.
Airship gets tangled in a giant tree, and begins sliding out (airship is also packed with explosives and greek fire), so players will obviously get the heck out of there, and will likely head back towards the site of the battle.
Where they will meet up with the other characters who will report that the whole battle just sort of started dissapearing all around them. Nothing vanished while they were looking at it, but after about an hour of fighting nothing was left at all except for their own bloodstains on the ground, and broken arrows that they had fired. No soldiers, no wounded, no trampled grass, nothing. (The time change in the past caught up to the future).
The (psuedo-npc) characters who had noticed the original anomoly village suggest that as something to check out. The player's travel there across a changed world, none of the towns or villages that should be there are there, and they will actually encounter a party of human merchants travelling to trade with the elves (these are non-human lands, and human merchants don't generally go to the elves, they will usually just trade with the first halfling village of the area, and then THEY will trade with the elves.
Back to the "village". The one remaining village has regressed even further (time change caught up completely with it). The haflings there know nothing of normal halfling culture, Littleman, or the halfling pantheon at all. "We don't have any gods, those are for the big people."
Back to the cave near the village, go through it to the spot where the halflings gave up before, move past it (insert general dungeon adventure here, notice evil orcs in a land that previously had good/neutral orcs). They find the message from Julie. They also find (amongst other treasure), an amulet that radiates magic. This amulet actually contains the big bad's essence.
Through a time portal. That ends in a nasty golem infested gauntlet. Find evidence of someone else having gone before. Find the invisible remains of "Sheriff Alex" towards the end, in a room that has a type of Golem that can see invisible creatures. Note, none of the Golems in the entire place will attack Megan (girl the big-bad was obsessed with) for any reason.
Out of the time portal into the primeval age.
Valley with Dinosaurs, large oversized mammals, unicorns, and wells, lots of wells. Creatures in the wells similar to Morlocks, but a lot stronger (they regenerate, the leaders have all the powers of Ogre Magi, and few others to boot).
Morlock thingies attack each and every night (after the first) until their numbers are exhausted.
Big bad sneaks in silently and invisible the first night and takes a small hair clipping from everyone. Disabling any guards with magic if needed. Big bad begins making clones with his limited clone spell. Big bad ALREADY cloned Megan 5 years previously from a hair clipping he took while he was still with the group, that one is a full clone (which is much harder to do and much more expensive).
Things of note scattered around the map.
Unicorn meeting encounter is scripted.
Various ancient/prehistoric encounters with little relevance to plot.
Characters discover and investigate the OTHER side of the portal, the one they came through in there own time, it is still under construction. No message from Julie there yet.
A Cyclops cave with a cyclops willing to talk for a while before trying to cook the characters "now get in the stew pot like good girl fairy tree hugs". No humans in this world, besides the big bad and the players, so most intelligent monsters will assume the characters are fairies of some sort.
Halfling village. Not really a village so much as a series of holes with naked pre-historic halflings hiding in them, who the Morlock things like to eat on a regular basis. 2 of the 3 halfling characters are scripted to leave the group (NPCS), to teach them how to be real halflings, thus becoming Littleman and Yondalla.
Characters meet the big bad, who is quite friendly. He shows them back to his place, tells them all about the world and his assorted adventures since they last parted (and explains what happened when they parted). Towards the end of the meeting (in his home) he asks that the female characters step outside for a few minutes (here, go give the Kobolds some treats, they will like that), so they can discuss some "male issues". He then presents a 25 year old Megan to all the male players. Both of them explain that the younger Megan cannot know, that forknowledge for her could have disasterous results. Players will assume that this really is the REAL Megan, just older, and not a clone.
Players leave, thinking plot is going one direction, when in reality the big bad is finishing up making his clones of the group, so that he can trick Julie into leaving the message, thus drawing the party back in time so that he can snatch the REAL Megan, because he knows the clone one isn't real, and she (being a clone) is sterile.
When clones are complete he teleports Julie away in the night, she awakens with her (false) companions in a mockup campsite. There is a wagon with a red door on it, they open the door (before Julie can say anything), and the big bad comes out and "captures Megan" (who is a clone), and "kills" everyone else (the other clones, who were teleported and not disentegrated like he claims they were), he then tells Julie, I have another disentegration spell for you as well, and he begins a spell, of course she runs. His spell is really suggestion, he "suggests" that she leaves a warning message, which she does.
Meanwhile at this time evil clone Julie is in the group, and evil clone Megan may or may not be as well (depends on how things are going).
Eventually they will figure the clone thing out, fight the clones (who are easy to beat for the most part, being imperfect clones, with fewer hit points and lower scores). Find their way to the big bad's real fortress (and get sidetracked on the way with a modified version of module G3 "Hall of the Fire Giant King").
That is as far as I have written. I haven't written the endgame yet, but eventually real Megan and evil Megan will get switched (evil Megan having drank a youth potion to turn back a few years so she can pass for real Megan). Evil Megan is not aware of the REAL plan, she thinks they want the real Megan so he can do a mindswap with them and put her mind in the REAL body, so that she can have children.
I already incorporated the Labrynth ideas into the game on the other side of the portal, they come out of the portal into the Labrynth-esque area.
In the endgame the player's should have to save Megan, face the Big Bad and the Evil Megan (who is a lot more powerful than the real Megan, being 5 years older and having spent that whole 5 years adventuring with the Big Bad in the high powered primeval era). Big bads research shows that the pre-human mind-flayeresque old ones who used to live in the jungle possible had the time stop magic he needed to get back to the present.
What the characters don't find is the clone of the big bad. He started a FULL clone growing the minute the characters came back. Figuring he will need it if he fails, or if he succeeds he can kill it before it wakes up (never let a full clone wake up in a world that includes the real one, they will mind link and head straight for each other with murder on their minds, Megan and Megan clone are safe from that effect because Megan clone woke up and lived 5 years in a time that did not include the real Megan). Clone wakes up, continues building his portal to bring the characters back in the first place, once it is complete he transfers his essence into the amulet that the characters will find. They will carry that to the past, and eventually back to the future as well, where he will have a chance at coming back again. Players won't find any of this out for ages, I don't plan on having the big bad come back for probably a REAL year. But I scripted it now to make it easy later.
Players look for old ones, ruins, yada yada, find a long term timestop scroll, and use it to come back to where they were before. They will overshoot by 3 years, coming back 3 years later. The world will mostly be back to normal, except for the (garbled) references to them in the halfling pantheon, and the fact that Kobolds are no longer a savage race at all, but have late Rennaissance technology, and worship "Blocky" the all encompassing cube (Megan's Diety, who was a personal Diety, but keeps getting spread around due to her time travelling prothesilyzing). Tech was caused by the Big Bad's Kolbold servants gaining middle ages level building and forging tech way too early from the big bad, religion is the fault of clone Megan, who told them all about Blocky.
Then from there they have to deal with the fact that in their 3 year absence the Big Bad from THIS time (a good leader, destined to go bad), has gone from good to neutral, wiped the Goblin race from the continent, built castles near every town in the realm, and has declared war on the spacefaring goblins as well.
Complicated and nerdy, eh?