When Spider-Man publicly unmasked in support of the Superhuman Registration Act, his family became a target for every member of his rogues' gallery. He thought what he was doing was morally right and was confident that Mary Jane and Aunt May were safe inside Stark Tower.
Over time, he grew to resent being forced to capture his friends. While transferring unregistered heroes, a change meeting with Captain America forces him to reevaluate his position. His decision was not made lightly, but it was made quickly. He convinces MJ and May to leave the safety of Stark Tower for fear that they will be imprisoned when he goes rogue.
Life as a fugitive is difficult but they make due until Captain America surrenders, ending the civil war. Peter returns to the motel room where they are staying and saves Mary Jane from an assassin's bullet. Peter was able to save MJ, but May was critically wounded and had to be hospitalized under a false name. The combined stress of the war and having May near death sent him into a downward spiral, which prompts him to symbolically wear his black costume while he finds the assassin.
In this reality Aunt May is not struck by the assassin's bullet.
In this reality when the sniper fires the fatal bullet into the motel room, Aunt May is standing closer to Peter than Mary Jane. When Peter's spider-sense goes off, he protects Aunt May. The bullet pierces MJ's heart, killing her instantly.
As the assassin contacts the Kingpin to confirm the kill, he is met by a very angry Peter who grabs him by the throat. He demands to know who sent him. Despite the extreme pressure on his windpipe, the assassin tells Peter it was the Kingpin. The assassin then pulls a gun on Peter, who rips it from his hands and shoots him with it. Peter is shocked to the core over what just happened. His wife is dead and he's killed the man who killed her. He blames Kingpin for this and returns to the motel room.
He explains to May what has transpired and she does her best to calm him down. Unfortunately he has revenge on his mind. Due to his fugitive status, he won't be able to even attend MJ's funeral. The issue is further complicated by the fact that the Kingpin won't face the legal consequences of his actions as in already incarcerated at Ryker's Island prison. Left with little choice, Peter pulls out the black costume and sets out to kill the Kingpin, despite May's pleading.
For his part, the Kingpin has already contacted the FBI and informed them of a potential attempt on his life, leaving out the obvious details of "why". The Kingpin is too valuable a resource to be killed outright so they make arrangement to protect him. These arrangements include securing the services of Iron Man to stop an unregistered hero.
When Peter arrives at Ryker's, Iron Man and SHIELD are waiting for him. Spider-Man is not in the mood to fight his former teammate; he wants Fisk. Iron Man is initially not interested in the reasons why Spider-Man is after Fisk until Peter tells him he was responsible for MJ's death.
After collapsing part of a nearby building on Spider-Man – which he admits will only delay him – Iron Man confronts Fisk about Mary Jane. Fisk doesn't admit to any involvement, only points out that she was aiding a known fugitive and should be held accountable in some way. Stark almost strikes Fisk for his actions, but reluctantly allows him to be taken into protective custody by the police.
While Fisk is taken away, Spider-Man digs out from the rubble and resumes his pursuit of Fisk. Iron Man once again denies Spider-Man any opportunity for revenge. Unable to take out his frustrations on Fisk, Spider-Man attacks Iron Man without reserve. Stark is caught completely off-guard when Spider-Man deactivates his armor. Spider-Man explains that he was able to analyze the "spider armor" Stark designed for him and found a design flaw. Since their armors are similar, he was able to exploit that weakness and subsequently knocks Stark out.
Spider-Man makes his way to the Newark airport where he finds Fisk. Fisk explains that the police officers assigned to him are on his payroll. For his next surprise, Fisk brings out Aunt May and informs Spider-Man that he will either allow him to beat him to death, or the cops will kill Aunt May. He considers this a "going away" present that will sustain him during his European exile.
Rather than playing this game by Kingpin's rules, Spider-Man kills Fisk in one punch and webs the cops to the hanger wall. He knew that May wouldn't be allowed to live as she is a witness. May is horrified at her nephew's actions and disowns him for his actions.
At this point Iron Man (in full armor) and other members of the NYPD arrive to arrest Peter. He symbolically surrenders to the police, not Iron Man. He tells Iron Man that he wants a trial and hopes for a sympathetic jury, but is willing to pay whatever price is required for his actions.
As they take Peter away he tells Iron Man that his only mistake was ever listening to him. As they load him into the squad car he states that " ... if I'd known what I was doing, I would've never married her".
AGH!!! A very tense story such as this needs a different type of ending than the one that was chosen. It's not Peter's decision to kill the Kingpin. It's not Peter surrendering to the police and demanding a trial. It's the final comment as he's loaded into the squad car about being married to MJ.
Perhaps I'm going a bit overboard, but the word balloon containing the last sentence clearly emphasized the word "her", meaning Mary Jane. This is not a story about what fictitious woman does or does not deserve to be Mrs. Spider-Man; it should be a straightforward story about what might happen if Spider-Man's wife was shot instead of Aunt May. The theme of the story is revenge, pure and simple. Going off-topic – even at the very end – detracts from the story.
When Gwen Stacy was killed by the Green Goblin, Peter reacted in a similar manner when he tracked down the Goblin and nearly beat him to death. The desire for revenge is understandable given the circumstances, both for Gwen and MJ. However it doesn't make sense that Peter would be willing to commit (another) murder to avenge his wife, only to wish they were never married.
I think that this particular comment was allowed due to Joe Quesada's anti-marriage stance.
3 webs. What started out as a very good story turned sour at the last minute. There were a few other minor problems with this issue.
First of all, why does he have the black costume at all? Why would he think to bring that with him? Much like in the original "Back in Black" storyline, Peter just starts wearing it again. I thought that he abandoned that particular costume after Venom's debut. It seems unusual that he would have one on hand.
Second, May accepts that Peter killed MJ's assassin but she disowns him when he is faced with the choice to kill Fisk or let her die? The inconsistency on this subject bothers me a bit.
And finally Peter would have the same reaction whether his girlfriend or wife were killed by one of his enemies. He is obviously saddened by the loss of someone he truly loves. However when Gwen died, he never regretted that they were together, he just blames himself in part for her death. Now we're supposed to believe that he regrets marrying MJ because she's dead?
In either case being the significant other of a superhero doesn't automatically grant any degree of invulnerability or other super-powers. This remains constant even as the nature of the relationship changes.