Alright, i'll break it down.
Dugalle kill himself shortly before the zerg swarm destroyed the surviving fleet. Samir is an agent of the Xel'Naga. The dark protoss are still arround, just in fewer numbers. In a secret mission Zeretul finds that Duran is making protoss\zerg hybrids, saying that is was destiny and implying that the hybrids were what the Xel'Naga origonally set out to create. Of course there will be hybrids on SC2, Xel'Naga i dont know. The Xel'Naga appeared to hav been killed by the zerg, but you dont think that such an advanced race would leave there entire armada in orbit over Zerus(origonal zerg homeworld), do you? The Zerg never assimilated the protoss, when both overminds died that directive was replaced with Kerrigans survival\victory.