The Capstone Research Project is intended to be one that integrates to some degree the coursework you have done in Philosophy. This is the reason for the general restriction to seniors, which is designed to guarantee that the student has sufficient familiarity with the field as a whole to produce a project that does exhibit some degree of integration of issues, approaches, and ideas.
The choice of the course in which to embed your project does not mean that the project must make use mainly of material pertaining to that particular course. For example, take a course such as Modern Philosophy. That course has connections with Medieval and Greek Philosophy by way of history and by way of ideas. It has connections Contemporary Philosophy by way of issues in epistemology, metaphysics, and ethics. It has connections with Philosophy of Mind, Philosophy of Science, Philosophy of Religion, Philosophies of the East, and so on. A student using Modern Philosophy for their Capstone Course may therefore write on just about any topic, approaching it from multiple perspectives, including that of Modern Philosophy.
Pick any major course in Philosophy and you will find a wealth of connections with other subjects and courses. Thus the goal of integration of a variety of course material is easily achieved, and the pressure to choose the "right" course in which to embed your Capstone Research Project is to some degree relieved.
It is important to start thinking early about where your interests lie. Start talking to your advisor and other faculty about possible projects before your senior year. In this way, when the time comes to actually do the Capstone Research Project, you will be able to hit the ground running. Below you will find a timetable for Capstone Projects that demonstrates the expectations to which you should conform during the semester in which you undertake the project. It is particularly important for graduating seniors to pay close attention to this timetable to ensure all graduation requirements are met.
Timetable for Capstone Research Projects