I had unprotected sex on my period and took the morning after pill the next day however now there is a smelly brown discharge, how do I make it stop?

Little you can do. It should go away on its own within a few days and there is really nothing you can or should do at this point. Do not douche. If it persists or the odor is particularly bad than you should be checked by your physician.
Go see your doctor. Smelly vaginal discharge is worrisome for an infection. Best to go see your family doc for an examination & appropriate testing w/treatment as indicated. That's the best way to make it stop. And assuming you don't want to go thru this again, make (all) your partner(s) wear condoms each & every time w/o fail.