The question is about how did the person who invented Grothendieck topoi (presumably Grothendieck) arrive at the necessity of a such a notion. I do not know much about the history of the subject. What I do know is that functoriality for crystalline cohomology is most elegantly done via the introduction of topoi and can not be always be done if you work at the level of sites.
So was this person solely motivated by the crystalline cohomology? Were the any other geometric, topological or number-theoretic (not set-theoretic or logical) problems that "forced" the notion of topos (as opposed to site) upon you? I am not asking for overly hypothetical justifications (for example, by notions whose existence was only discovered well after Grothendieck topoi were introduced) but the justifications by problems which could reasonably be of interest to people (that is, already were around and had not yet received a completely satisfactory treatment at that moment) in 1950s and 1960s. If the justifications you propose were explicitly stated as motivation in the research literature of the era, that is even better.
The question is somewhat speculation-ish but not overly so. It still is answerable, just give relevant examples of problems and how Grothendieck topoi come up when you try to solve them.