Originally Posted by Marvel Wiki
Spider-Man disappears after the battle and makes his way to the motel room where he, Mary Jane, and Aunt May live in. As he is welcomed by his loved ones, his spider-sense rings and he quickly hits the floor with Mary Jane. Unfortunately, in the act of saving one, he has lost the other, and Aunt May is shown bleeding from the left chest, indicating a fatal wound.
The Civil War wraps up with a majority of the Secret Avengers accepting the general amnesty given. However, some have opted to move to Canada while others join an underground rebellion against the Superhero Initiative, which appears to be headed by Spider-Man and Luke Cage. They are last seen with Cage complementing Spidey's suit, and we are shown the inevitable truth: Spider-Man is back in black.