Hello and welcome, it's that time again! Sudura2017's crappy theories!
Here's the canonical layout of the DS world (made in GIMP, looks like Paint. - No MS Paint for Mac. What is this blasphemy?)
Now that that horrible thing is out of the way, let's get into the lore.
We'll start from the beginning, the Ancients (since they did not die all too soon...)
The Ancients live peacefully on the Mainland
Get the dumb idea to mess with black magic in a time of hardship
Abuse Nightmare Fuel for food and other items to build a sprawling city
It's all erased and the Ancients become the Shadows. Sucks for them.
Ancient Guardian/Staff Guy 1 is now on the Throne!
Walani, Warly and Woodlegs enter of their own accord to the Archipelago, through the Bermuda Triangle.
Wagstaff/Staff Guy 2 enters, likely through his research on the Shadows, As he made WX-78, there's a high chance he came too. Not that WX would care. Stupid fleshling madness.
Wagstaff/Staff Guy 2 takes the throne from the disgraced Ancient King/Guardian/Staff Guy 1
Wagstaff calls in some survivors, notably Webber/Wes/Winona (and possibly Wilbur) due to the fact they were dead/locked up/in the game pre-DS, more than likely from a circus and his enemies/useful employees. A mime, a circus freak and a monkey assumed to be a Circus animal (William Carter puzzles) + Winona, an ex-Voxola employee.
Around here, Maxwell enters!
Maxwell accesses the Throne Room via the Ancient Gateway using Wagstaff's Divining Rod (hence his quotes, and Maxwell's Door is not built yet.)
Maxwell takes pity on Wagstaff, releasing him from the throne.
Maxwell takes in the characters, minus Wes/Webber/WX/Wilbur/Walani/Warly/Woodlegs and finishes with Wilson.
Wilson/the others survive for a while before trying to escape by boat, ending up stranded in the Shipwrecked Archipelago.
The Seaworthy is repaired, perhaps by Winona, allowing them to go back to the Mainland. They do, however, this appears to split them up.
Maxwell gets released by Wilson from the Throne.
He is missing for a while...
Wilson gets released by Charlie from the Throne
Wilson works on blueprints for a Portal to link these dimensions.
Maxwell eventually appears in Wilson's world, possibly at Charlie's decision.
Maxwell shows Wilson his own blueprints for a Portal, likely designed by Wagstaff or by Maxwell, after the Ancient Gateway.
Wilson and Maxwell put aside their differences and build the Jury-Rigged Portal.
Wendy, Wes and Wolfgang enter, before Charlie destroys it to make a Florid Postern in it's place.
There, a timeline!