Siren 2 is themed around sci-fi-ish parallel worlds, diverging into countless possibilities. In order to unravel the mysteries of its subplots, you must have a certain level of grasp on the connection of time and space, and its correlation.
Long, long before the dawn of humanity, in a distant age, the world was created through the death of Annaki, the being with which everything began. The bones of the unique being turned into countless tiny fish (which is why Annaki itself does not exist), many of which passed into the real world. One of these turned into "light", and flooded the world with light (Flood of Light legend).
However, at this time the earth was inhabited and controlled by beings unlike humans - the "ancient ones". Having no resistance to light they were chased across the land, fleeing to the Other World (World of Nothingness). They finally lost their corporeal forms in the chaos of nothingness, fusing into a single consciousness - Mother - for a near eternity, and falling into a deep sleep. Some inhabitants remained in the real world, but they lived like ghosts at the bottom of the sea where the light could not reach them, surviving by taking the form of Shiryo. This is how the ancient ones completely vanished from the earth's surface.
The cause of the strange events that occur in Siren 2 is the awakening of Mother due to the effects of environmentally-damaging construction occurring on Yamijima. Taking the image of the drowned body of a woman who washes up in the World of Nothingness Mother, now possessing a form, creats a copy of Yamijima in the World of Nothingness (to act as a foothold into the real world), and begins searching for a way above ground (releasing offshoots - doves - of herself). Eventually, Mother comes to believe that she requires an "olive branch" (a human shell) in order to live above ground. Thanks to the Return of the Dove, Mother (entering a human shell) begins to birth Yamirei in order to regain the earth, her old homeland.
Viewed by the driven out Mother, a former ruler of the world, who has an absolute - and perhaps even unreasonable - power, we humans most likely seem to be inferior beings who have taken over her home while she was away. The two conflicting sides begin a fight for survival, Judgement Day coming after several hundreds of millions of years. Perhaps this is another case of a god's teasing.
Annaki no longer exists in the real world. It left behind tiny fish/various beings, all of which turned into "something else"... or so it is said. Since it is a being that surpasses human comprehension, it is impossible for humanity to fully grasp precisely what it is. Archive [No.056] UMA Fossil is another of these.
Mekkoju, Pylon (Spider's Thread)
The Mekkoju is a tree that existed in the World of Nothingness, and manifested in a physical form when Mother created the Reflected World. Since it is a phenomenon where it became a special existence (place) after being speared by what used to be a bone of Annaki, it merged with the pylon built on the forbidden ground on Mt. Shinari to manifest as the "spider's thread". Also, the effects caused by its collapse cause the "Singularity".
A power - or phenomenon - that allows a person to intentionally steal a glimpse of the vision or hearing of someone else. Each of the people trapped in the Reflected World obtains the ability to have these "visions" due to the influence of Mother's power, who uses clairsentience to communicate with Offshoots and Yamirei. Since Mother and Otoshigo were originally of the same species, Yamibito and Shibito are also able to have visions due to their collective consciousness.
Mother, living in the World of Nothingness, repeatedly uses a red tsunami to drag people from the real world into the Reflected World. In the game it appears as though people are brought from three time periods - current day, 29 years ago and 19 years ago - into a single world; this is because they are swept into Yamijima, an area of space-time created by Mother, regardless of time period. The Reflected World simply constantly restores ("backs up") itself to the way it was when it was copied from the real world, preserving its form (if it didn't, it would be erased by the chaos of nothingness).
Also, the "display times" shown in the game are not definite times but rather the amount of time that has passed as the characters experience the event. Furthermore, when time is rewound by Mother's power at 6:00 "Return of the Dove" (they return to six hours earlier, and midnight falls once more. This is why the night seems to last for so long), it causes the correlation of time between reality and the Reflected World to become vague.
29 years ago the Reflected World became sealed away within time and space, but since those sent there are not beings created by Mother even the smallest of their actions have a drastic impact on the entire world. When events that will have a large bearing on the future occur, the Reflected World shifts to a world in which there are as many worlds as there are possibilities, and another, new future - a parallel world - is born. Mother's wish to return above ground and her "emotions" resulting from this cause the rules of the World of Nothingness to warp, creating infinitely diverging parallel worlds. Of course, there is the possibility that in one of these worlds there exists an "opposing power" to contain the flood of parallel worlds...