> it is widely believed that eukaryotes arose from a joining of archaea and bacteria, not archaea and virii

IIUC the join with the bacteria is the explanation of the mitochondria (and later chloroplast). But it does not explain the nuclei that is weird too. Is it possible something like this?

  Archaeal + Virus = Pre-Eukaryote (extinct?)
  Pre-Eukaryote + Bacteria = Eukaryote (including animals, fungi and plants)
  Eukaryote + other Bacteria = Plants

(Or swap the first two steps.)