The following spoilers are from tomorrows Spider-Man #1, written by JJ Abrams.
So the story starts off with what appears to be a battle. MJ is involved and is killed and tossed to the side as Spider-Man rushes to catch her. The scene depicted definitely gave me the impression of when Gwen Stacy was killed and toss off for Spider-Man to catch and attempt to save her.
12 Years Later... Peter has to respond to the school calling after Ben gets into some trouble. We find that he has a missing arm.
It's reveled that Ben is now living with Aunt May, when he discovers some abilities....
Aunt May gives Ben a box to go through to learn of his parents and past..
Where he then discovers the biggest secret of his father...
Some are saying this could be Ben Parker from Spider-Girl #59. But in that story, MJ is still alive. I think this is an entirely new timeline and or story, which could result in it being a first appearance of Ben Parker discovering that his father was Spider-Man.