Endosymbiotic Theory
The Endosymbiotic Theory of Eukaryote Evolution (Symboitic Theory) was first proposed by former Boston University Biologist Lynn Margulis in the 1960's and officially in her 1981 book "Symbiosis in Cell Evolution". Although now accepted as a plausible theory, both she and her theory were ridiculed by mainstream biologists for a number of years. Thanks to her persistance, biology can now offer a plausible explanation for the evolution of eukaryotes.
The theory maintains that ancestors of eukaryotic cells were "symbiotic consortiums" of prokaryote cells with at least one and possibly more species (endosymbionts) involved. 
In other words, perhaps oxygen breathing bacteria invaded an anareobic amoebalike bacteria, and each performed mutually benefiting functions. The bacteria would breathe for the anareobic amoebalike bacteria, and the amoebalike bacteria would navigate through new oxygen-rich waters in search of food. This way, each of the organisms would be benefiting from their symbiotic relationship as the waters and atmosphere of the Precambrian changed.In support of this, notice that oxygen begins to accumulate between the first fossil records of Prokaryotes and Eukaryotes.
http://facstaff.gpc.edu/~pgore/students/w96/joshbond/symb.htm
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