After the Scorpion (who seems to be a clone of Peter Parker) is knocked unconscious in the previous issue, Spider-Man takes him to the Fantastic Four to try to find out what is going on.
Reed Richards put the clone through a DNA test, and discovered that he was a 94.2% match to Peter Parker. And Susan Storm found that the tail mechanism was grafted onto his spinal cord, which she revealed to be illegal.
To see if they could find out what was going on with this supposed clone, Reed contacted Nick Furry, and asked him if he knew anything about cloning experiments going on anywhere throughout the world, but he didn't and this only made him suspicious.
Spider-Man realized what time it was (issue does not specify time), and says that he must leave, or Aunt May will ground him.
Peter came home to find that Mary Jane is missing, and immediately leaves to find her.
The first place peter checks is her house, they show marks on the wall (hand and foot prints) from someone like Spider-Man climbing up the wall, but no one sees them.
He runs out of her house, and goes to their secret hideout, the warehouse. He climbs up the wall and jumps through the window. He doesn't find Mary Jane, but he does find a girl in a Spider-Man costume, but the top is open for her hair, and it's black with a big white spider on it (see cover).
Peter is very aggressive and rude in his conversation with her, and ends up lunging at her, but she jumps out of the way using abilities equal to his. He lunges again, and she dodges again. Then to stop him, she punches him in the face and throws him at a post. He throws something at her, and she maneuvers her head away from it, then webs his face with an organic webbing (similar in consistency to his) emanating from her index finger. She checks to make sure that he's alright, then she basically says that she's sorry for coming there, that the confrontation was her fault, and also that she is going to fix things, and get back at "them". "We didn't deserve this", she says, and then she swings away.
When Peter wakes-up, he thinks that maybe Mary Jane could have gone to his old house. But when he gets there, he sees that the door is open, and that Gwen Stacy is inside in her pajamas (alive and well), but she doesn't know of anything after and including her death.
Mary Jane wakes up inside of a glass container, with a man who appears to be Peter Parker outside of it. He tells her that he is going to make sure that no one can hurt her ever again, but she screams for him to let her out.