There are a number of thoughtful research angles you might use to investigate apartheid. For a compelling research project, it's best to consider what interests you most about the subject—taking care to stay within the bounds of your assignment—and then develop your inquiry from there.
If you're interested in looking back in history, you might consider tracing apartheid's roots as far back as you can to look for contributing factors. Like most systemic institutions, apartheid didn't occur in a vacuum. It was a response to a long, complicated history that began way before the system was formalized. An example of a research question for this inquiry might be, "Which earlier events in South Africa's history contributed to the rise of the apartheid state?"
If you're interested in apartheid in a global context, you might consider looking at how it resembles or differs from other instances of segregation and state-sanctioned racial violence throughout history. One possible example would be to see what similarities or differences you find when you contrast apartheid with segregation in the United States or with the machinations of the Holocaust. Possible research questions for this line of inquiry might be, "How does South African apartheid compare to legal segregation in the United States?" or "What similarities does South African apartheid have to the Holocaust?"
If you're more interested in the present day, consider looking at the lasting impact of apartheid on modern-day South Africa. What legacy has the system of segregation left on those who still live there? For this inquiry, a possible research question might be, "What lasting effects from the apartheid system persist in South Africa today?"