You should address the theoretical implications of your research after the introduction. Find outside sources that deal with your paper topic and discuss how they relate to your own unique research. Explain your theory in a step by step fashion. Lay a foundation for your argument that is persuasive. You will also want to discuss arguments that go against your theory, and explain why you think your theory is better at explaining the dependent variable.
All researchers make assumptions about their work.
When you explain your hypotheses, tell the reader what you are assuming or not controlling for in your study. Make it very clear how you expect the relationship between the independent and dependent variables will respond. Look back over one of the political science articles we handed out in class. Notice how the paper is layed out. Be sure to divide and head your paper into similar sections.