They got sucked out of their respective universes by Polygon Man. They are at the PlayStation's most basic state. They fight each other and Polygon Man just for the he|| of it. Then they go back to their universes and pretend like it never happened.
Omar already answered this in the recent IGN interview: Theres a part in your PlayStation where they come together. Dont expect any more of an explanation then that, especially not from the arcade mode.
Polygon Man is a crazy uncle holding a family reunion, but everyone has "that one" relative they can't stand. Things get out of hand and Polygon Man trys to settle everyones differences but they won't listen so he has to beat the crap out of them. He's a misunderstood fellow. Duh