Dark Cloud/WMG
The Sun Atlamillia and the Sun/Pez Sphere are the Same Stone
All you need to look at is the number of years between creation of a Sun Sphere on the Sun and the number of years the Sun Atlamillia can travel, either direction, through time. They're both 10,000 years. Caught in the evil Dark Cloud below Dark Heaven Castle, the Sun Sphere absorbed the evil energy, losing its green stripes and became pure yellow. Like the "lucky" rat, the Sun Sphere absorbed some of the Dark Genie's power.
Alternately, the Sun Atlimaillia is A Sun Sphere
Again, see the 10,000 year cycle.
Someone in Dark Cloud 2/Dark Chronicle is a Time Lord
With all the time travel, it's bound to happen.
- It's probably Osmond. Hell, he's probably the one who convinced Seda to mix his blood with the Witch Species.
Palm Brinks is a combination of Queens and the Demon Shaft
High above the ground (Demon Shaft), mostly walled (Queens), and check out the scroll work on the town gate.
Sheriff Blinkhorn is Wilder's descendant
Monica Raybrandt is part genie
She has the same Power-Up Food as Ruby.
Xiao was originally owned by someone who lived in Norune village. Her owner died in the Dark Genie attack.
Every time Toan meets her before recruiting her, she is already wearing a collar. Unfortunately, Fairy King Simba was not powerful enough to save her original owner.
Monica Raybrandt is Max's great grandmother
With the big time pretzel going on, and her stuck in Max's time it makes sense. She has a kid whose kid turns out to be Elena. That'll bridge the 100 year gap, and make her Max's wife and great great grandmother.
Monica2 is The Girl In The Street
After the events of Dark Chronicle/Dark Cloud 2, Monica uses a Starglass which returns the user to a time of great significance to them. When Lin's starglass took her to the day Crest was killed, we get evidence of both Lin1 and Lin-A in the same time, granted in different places. The reason people who aren't traveling with you know things is because Monica2 has told them about your adventures on her way to Palm Brinks and the Zelmite Mines.
Toan's time is Before Monica's, but after Max's
Just think about it, You have to do many changes to the landscape to revive Jurak in #2, yet you only have to create a river to revive him in #1. Palm Brinks eventually becomes abandoned (more on that later). Osmond in the first game was not at Luna Lab because it didn't exist yet. (Luna Lab was founded after Shingala brought a huge haul of Luna stones 27 years after his rescue.) Mt. Gundor was demolished somehow (which would explain why you barely see the volcano in Monica's time) and Gundorada workshop was not built yet. Winds from the sea blew sand over to the no longer mountainous area, forming the desert, Muska Lacka was actually just a temporary camp while they were making preparations for Gundorada, and eventually Paznos. Then An earthquake happened to happen right near Gundorada when it was just a foundation, forming the mountain that was carved to create Gundorada. Toan's village was probably a group of settlers that came from Palm Brinks shortly after the end of Dark Chronicle, and they decided to make a settlement in the area they found. The fairy king is probably a mix breed descendants of the Firbits and humans, seeing as he's a fairy but also looks very human. He also has that silly mustache.
- Much of that makes an amazing amount of sense. Vennicio's cave crumbles and becomes the walls of Queens. Palm Brinks, which is already pretty damn high above sea level must have a fault line between the city walls and the Zelemite Mine area. An intense earthquake splits the two locations from each other, with the walled area becoming the Demon Shaft, though how it starts flying is beyond me. So Max' time is Dark Cloud -1, Toan's is DC 1, and Monica's Original Time is DC 2. This also would explain how Seda know of Atlamilla existing before his time. Furthermore, what is the Mayor of Norune's house? A crashed airship, and he tinkers with machines according to one of the female villagers. Perhaps he's working on bringing back the old technology?
Toan and the others NEVER returned to their own time
Seda says he's going to improve the world. He supposedly has amazing magical power even without the Dark Genie. After rebuilding both continents, Seda either creates a fabrication of what Toan and Xiao remember, or makes these places exist earlier.
- No he sent them back to their original hometown in their correct timeline. Unless you can provide something to support your logic?
- The events that created the original timeline got erased: Temporal Paradox.
All four Altamillia are part of some divine cycle of death and rebirth.
Though this can be Jossed easily due to different sources -the Fairy King grants one Atlamillia to Toan, while the other three are suggested to be crafted by the Moon People- hear me out. These Atlamillia all have a predestined function. The green stone -some say it's blue, but it always looked blue-green to me- is the Altamillia of "history", or "records", keeping the fragments of the world together within it. The other three, Red Earth, Blue Moon, Yellow Sun, symbolically represent the events that will lead to the "Star of Obilivion". He who bears the yellow stone gathers them together, and thus the Blue Moon shall fall and the earth with be consumed in the fires of destruction...
After all is said and done, the earth is 'reborn' through the Atlamillia of the first game.
- The trick to noticing Toan's Atlamillia is blue is to look at it while he's climbing a ladder. It appears green when you release an Atla because it's reflecting his turban.
The war that Seda fought in was against Alexandra's nation
This theory is explored on the official Dark Cloud wiki under the heading "Dark Cloud History". Because of the Timey-Wimey Ball, it is mentioned as a branch from a timeline.