Pretty much what we've seen before. I've read Margulis, but she's apparently hardened her stand since she made the major discovery that mitochondria and chloroplasts are endosymbionts. From that, she concluded that most or all organelles are such, but that didn't work out to be true.
From one observed case of endosymbiosis, the evidence shows that mutation and natural selection was the mechanism by which it happened:
Bacterial endosymbiosis in amoebae
Trends Cell Biol. 1995 Mar;5(3):137-40.
Jeon KW
Abstract
The large, free-living amoebae are inherently phagocytic. They capture, ingest and digest microbes within their phagolysosomes, including those that survive in other cells. One exception is an unidentified strain of Gram-negative, rod-shaped bacteria that spontaneously infected the D strain of Amoeba proteus and came to survive inside them. These bacteria established a stable symbiotic relationship with amoebae that has resulted in phenotypic modulation of the host and mutual dependence for survival.