These are some of my ideas, although a few of them are more plot related.

1. The Two Worlds. Two worlds, Earth, and the other, every thing Monster Rancher related, interlinked by a invisible barrier. Rarely, a hole appears in the barrier, allowing entrance into either from the opposite world.

2. A CD equalivelent of the Shrine, invented by in-game character. It reads the data from a CD, and uses it too create a Artificial Monster.

3. Monsters created from a CD. They are not exactly real monsters(artificial), therefore they have weaker stats, lesser life spans, though can perform feats normal monsters cannot, in terms of social status; they are like clones. They however can be manipated, which can lead to horrible consequences.

A mysterious form of energy that has been recently discovered. They come in various kinds, from Fire to form of a pure breed. A small amount exists in normal monsters, while none in artificial ones; either form of monster holder can be converted into Disk Energy. When large amounts are exposed to normal monsters, it causes a evolutionary like change, massive in terms. However, when exposed to artificial ones, it causes them to go unstable, turning them feral.

That's it, I suppose.