That's what always bugged me.
The lore was great, but it was hidden on the official website for Killzone 1.
The Helghan company was the first to colonize planets. They colonized a planet next to Helghan (Vekta) and worked on Helghan.
But they were like a gateway for intergalactic trade and got into a political dispute with Earth as they became too powerful economically.
So the ISA were sent in to take over Helghan. The Helghast lost the first war and were treated like shit and forced to live on Helghan, where they evolved to adapt to the harsh environment. Then KZ1 started with the Helghast preparing to reclaim Vekta, which was rightfully theirs.
Basically, the ISA are the bad guys. Or at least, it was all grey instead of B/W and the ISA being the heroes.
GG should've put way more effort into the lore, but that was one of the main complaints about the franchise.