How, indeed, can we go from a prokaryote to a eukaryote. For some good ideas on how this could have happened check out Lynn Margulis's work. She is the originator of the endosymbiont theory, but also considers the origin of the nucleus and chromosomes. Again, I implore, I beg, I plea, I lay prostrate on the ground beseeching you to produce an alternative to evolution by descent. That's not how science works.
Science is analogous to a murder mystery.
You take all the evidence you can find, and then try and make the best case that you can. The judge and jury, in science, is the scientific community and the trial never ends, in fact the investigation never ends, the case must be tried over and over again. The defense has found some gaps in the record, some disagreement about the exact nature of the killing. The jury is not exactly sure how the victim was murdered but there is definitely a corpse. The inability to see a beautiful theory if it bit you, with beatifully evolved jaws, derived from gill arhces, in the flesh that surrounds your atavistic tail bone, the cocyx.