Yes, you should have an Add/Drop form signed by your thesis advisor and bring it to the registrar's office. They will add the class to your schedule. You will receive one semester course credit (4 credits) for every semester that you are registered for a thesis.
In order to be eligible for departmental honors, a majority of departments require students to register for two semesters of a thesis, designated by the course number of "99." Some departments require that students register for a "99d," a two-semester, 8-credit course. You register for it in the fall and it will automatically roll over to appear on your spring schedule too. Generally, a grade of "S" (satisfactory) is submitted after the first semester as a place holder. The "S" will not affect your GPA. Once you complete the second semester, a grade will be issued, and that grade will replace the "S" and will also appear next to the spring "99d" course. That grade is factored into your GPA twice (once for each semester).
Other departments have their students register for a "99a" in the fall and for a "99b" in the spring. Separate grades are given for each course and they each count for one semester course credit (4 credits). Check with your department to find out how the "99" courses work.
Students must have a faculty member from their major department as their official thesis advisor. If they have several majors, they may have an advisor from any of the majors. Faculty from a minor may not be the primary thesis advisor. Sometimes students have staff members, faculty from other departments or people not affiliated with Brandeis as secondary advisors, but the primary advisor is responsible for submitting a grade and must be Brandeis faculty from the student's major department.
You should speak with your thesis advisor and discuss your situation. If you both agree that it is appropriate to not complete your thesis, the second semester can be dropped. Although the thesis will still be listed as a "99" on your transcript, you will not be eligible for departmental honors. The basis for grading the work done during the first semester will vary depending on the field and nature of the thesis, and this will be decided by your thesis advisor in consultation with others in the department. In some cases, a grade will be issued based on the work you have already completed; in other cases, the instructor will require that you write a paper summarizing your research. If your thesis was registered as a 99a and 99b you can drop the 99b as you would any other class (paying close attention to drop deadlines). If it was registered as a 99d then you should fill out an add/drop form and bring it to the Registrar's Office.
Departments award "Honors," "High Honors" and "Highest Honors." The method varies depending on the department. Both departmental honors and Latin honors appear on your diploma and on your transcripts.