This is what happened so far.
In hoenn, that is, I haven't paid much attention to the other regions.
Zero was chasing some humans, and killed one. The other escaped.
Ze slasherz mount an attack on an unspecified base.
Zero has a flashforward, and the escapee has it too. She faints and he captures her.
While in a boat, they get sucked into an Abyss.
Due to several loopholes in Arceus' and Darkrai's code of existance, Zero, his pokemon, and the girl get sent to Maintenance Island, and Zero has a soul now.
The robot President makes a declaration that they are now making robots out of an organic material supplied by Darkrai, making them much tougher to defeat.The robots are now effectively under Darkrai's control.
All humans except Ze Slasherz and any others that manage to escape are turned into robots.
Spike and Alex get into some mischeif and catch a Rotom.
Spike gets partially robotized.
Spike and Alex find Zero and the girl, Faith, and set off in hopes of landing in Jhoto, and capturing Celebi.
My summary leaves off here.