Formulate a thesis statement. It will not be enough to state that religious tolerance is important to the world or to global politics or peace. Your adviser will insist that you make a specific statement vis-à-vis religious tolerance, such as "Islam has a history of religious tolerance which might be called on to combat religious extremism."
Look for sources about the religion or religions in question, if you do not have a thesis statement on hand. Reading about the history of religious tolerance --- or lack thereof -- in a religion's history will help you formulate your thesis statement. You can start your search at your university library's catalog. Google Scholar and JStor to review academic books and papers available to students with university IDs.
Glean the evidence that you will use to support your argument. You will need specific historical examples of religious tolerance to prove your point. You might, for example, point to the history of Jews and Christians in the courts of Andalusian Muslim rulers to claim that Islam has a history of pragmatism in the face of religious minorities.
Write an abstract including your thesis title, a quick summary and your list of works cited in your thesis and submit the abstract to your adviser. He will need to sign your thesis abstract before you can submit the proposal to your department.
Hand in your signed thesis abstract to your academic department. The department will need to know that you are working on a thesis and you are planning to finish your degree. Some graduate students eventually drop out of the program and never write a thesis.
Organize the presentation of your evidence. You will need to open with an introduction that discusses the basic topic of your thesis, how you intend to prove your case and where you intend to take your argument. You may structure your paper however you see fit. For example, you could structure examples of religious tolerance in Islam chronologically or geographically.
Organize your conclusion. Once you have presented your examples of religious tolerance in Islam, you will need to explain why these are important and how they might be used to combat religious extremism.
Run a spelling and grammar check on your completed draft and submit it to your thesis adviser for review. He may request revisions.