A. the individual development of biological organisms, from embryos to adult forms, to have passed through all the previous evolutionary stages from single cell organism to its species ---
that is missing B. the individual development of biological organisms, from embryos to adult forms, to pass through previously all the evolutionary stages from single cell organism to that species---
that is missing. C. that the individual development of biological organisms, from embryos to adult forms, passes through all the previous evolutionary stages from single cell organism to the species of these organisms --
This is the correct choice, since all scientific theses are finally about universal truths and not just evidences from which the truth is drawn and hence a present tense verb such as passes is required.
D. that the individual development of biological organisms, from embryos to adult forms, previously pass through all the evolutionary stages from single cell organism to their species ----
“pass through” is S-V agreement problem
E. that the individual development of biological organisms, from embryos to adult forms, had passed through all the evolutionary stages previously from single cell organism to the current species --
had passed is wrong tense. May it was so in all species that were in the past years. But the passage talks of current species. So a past perfect has no place in such descriptions. Obviously the answer is C.