The hypothesis that Eukarya arose from one Prokaryote engulfing another Prokaryote to form organelles like the nucleus, mitochondria, chloroplasts, and possibly flagella. One scenario that is currently believed to be likely is a gram negative Eubacteria cell that had lost it's cell wall engulfing an Archeobacterium to form the nucleus.
This hypothesis is supported by mitochondria and chloroplasts having their own genome and the presence of a double membrane enclosing these structures.