During your first year of study the classes you take should be decided by you and the Graduate Director, after you first year you should have a submitted a PhD Plan on GradPlan where all the of the classes that you and your committee discussed are listed. During your initial guidance committee meeting you and your committee will decide what courses you need to complete, please consult your PhD plan every year when registering for your classes.
If your committee decides that you need to take any independent study course (HST 890 or 990) you will need to put this on your GradPlan, you and your committee should decide which leve, 890 or 990, and how many credits. You may only take 6 credits of any 890 course and 12 credits of any 990 course, so if you do not have an MA you will need to be sure to add 1 credit of HST 890 on your plan to take the semester you turn in your MA equivalent paper. In order to register for independent study courses you need to fill out an Independent Study Form. This form is electronic located at reg.msu.edu, under Student Resources > Forms > Student Instructor Form > Application for Independent Study. Once the form is completed it will be routed to the instructor for approval, then the department in which the Graduate Secretary will complete the registration.
All PhD students need 24 HST 999 credits to graduate, you may start completing these credits once you have finished your required coursework. To register for HST 999 email Elyse Hansen firstname.lastname@example.org, include your PID, the number of credits you would like to take, and the semester you would like to take them. If you are ABD you only need 1 credit to be considered a full time student, if you have taken all or most of your 999 credits and ask to be enrolled in more than 1 they will be denied unless there are extraordinary circumstances.