A hypothesis is, essentially, a thesis statement. The hypothesis of a dissertation is that question that inspires the Ph.D. student's research. It should be concise and answer one question and one queston only. Otherwise, the dissertation writer will lose focus in the process of proving too many different claims. A dissertation on Iran's modern political system might hypothesize that Ahmadinejad draws his religious inspirations from specific sources. The paper should then proceed to detail those sources and how they influence Ahmadinejad's policies.
Start by reviewing the literature written by other scholars on the subject. This helps the Ph.D. student to know what has already been done and what research areas are open to explore. It might also help a student to formulate views in opposition to those of another scholar. These views will help a student to write a paper refuting that scholar's claims. Once that is done, the student should do independent research. This research might be book work or it might rely on grants to travel to a place and explore a topic in depth in its original environment.
The research process will help a student to formulate and clarify a hypothesis statement. A Ph.D. student might approach the dissertation process with a potential hypothesis already in mind. A student should certainly have a hypothesis in order to write the dissertation proposal prior to writing the actual paper. Once the research is done, the writer will possess not only a clear hypothesis but also support to prove it.
The last step in the process is to prove the hypothesis. Essentially, this is the dissertation itself. A writer may choose to review scholarly literature in the first chapter of the dissertation or to insert it into the regular dissertation analysis. Either way, other scholars' conclusions on the subject should be present somewhere in the paper. The paper should introduce the hypothesis in the first one or two paragraphs and then use the following chapters to introduce the student's evidence supporting that hypothesis. The program may require an oral defense of the dissertation in front of faculty.