In what issue did Spiderman and Mary Jane break up?

Answer 1

if you mean in the comics and the most recent break up (there have been several over the years and that's an understatement) it is because when spiderman unmasked to the world, everyone he ever put in jail began hunting his family. this resulted in peter and Mary Jane living like Gypsies for a while and eventually aunt may being shot and put on her death bed. feeling his typical guilt, peter Parker blamed him self and his unmasking for this, and basically considered his life over. the marvel devil Mephisto preys on this guilt and offers him a choice in hopes of destroying him. he offers to return things back to how they were (before peters unmasking... and aunt mays shooting) if he allows him to wipe his marriage from history, (this is in the belief that without MJ peter will not be able to cope with life). Mary Jane talks peter into this believing that their love is strong enough that they will end up together again.

well they take the deal and everything is ok now, except Mary Jane was very very wrong, and she refuses now to be with Peter because she feels if he is ever unmasked it will be more then just a danger to her self but will also be putting her family at risk. (stupid reason right?)

if you are asking about the movies, it is because Harry forces Mj to dump him or he says he will kill Spiderman. Mj agrees to this, even though Spidey could kick Harry's butt... because peter is neglecting her and totally self centered. later he hits her... under the influence of the venom symbiote (not relevant to the break up but something i wanted to point out)

they hint that they are getting back together at the end of the movie...

Answer 2

in ultimate Spider-Man vol.13 peter breaks up with Mary Jane.