The Precursors meant to return and destroy the Forerunners for driving them out of the galaxy and bringing them nearly to extinction. However, during the process of trying to regain there full physical form, the Precursors pretty much transformed into the Flood. They then sought to destroy Humans and Forerunners so that neither will rise up against them ever again.
At least I think that's how it went down, I could be a bit off but I bet Mingy's new "Halo's story" post that got stickied will explain most everything.
"Did you just say that you respect pedophiles?" - butsizzle "Hell yeah." - _Sawyer