PREVIOUSLY: When the U.S. government passed the Superhuman Registration Act, Peter Parker came out in favor of the new law and revealed his secret identity as Spider-Man to the world. But after reconsidering the cause he had chosen to support, Peter switched sides to oppose registration, and joined Captain America in the fight against the government forces led by Iron Man. Now, the repercussions of Peter's decisions are coming back to haunt him.

Because Peter's identity is public knowledge, his wife, Mary Jane, and his beloved Aunt May have become targets of the world's most dangerous criminals. Recently, May was shot by a sniper's bullet, and now barely clings to life. This has led Peter to don his black costume as a symbol that he is not the hero he used to be. And Peter himself is a wanted man, on the run from the law enforcement agency S.H.I.E.L.D.. His fugitive status has also implicated MJ and May, for aiding and abetting his escape.

Earlier that day, Mary Jane (incognito) makes her way into the Coffee Bean to grab a cup of Joe. While there, she is accosted by an old boyfriend of hers, named Brady O'Brien, who recognized her despite her disguise. Apparently, this Brady guy has relocated to New York City to do some security work; he offers to buy her a cup of coffee. MJ reluctantly agrees. As they sit at one of the tables, MJ comments that there is a new guy working the register. When Brady asks MJ how long she has been coming to the Coffee Bean, we are treated to a flashback to years earlier when MJ, Harry Osborn, Peter, and Gwen Stacy used to hang out there together. Back then, MJ used to date Harry and Peter was with Gwen. Back in the present, MJ answers that she has been coming there forever and apologizes to Brady for daydreaming in front of him. She proceeds to ask Brady to tell her about his security job, prompting him to reveal that he is none other than a S.H.I.E.L.D. agent and that she is under arrest unless she gives them Peter.

In another part of the city, at Hopper's Diner, Peter Parker has arranged to meet with Detective Lamont of the NYPD. As he sits down at the table next to Lamont, Peter (wearing a fake moustache) tells him that he wants to give himself up in exchange for total immunity for his wife Mary Jane and his Aunt May, who is clinging to life at County Memorial Hospital. Peter simply has had enough of running away from the law and consequently forcing his family to hide to protect him. His whole life, these women have been there for him and now he wants to be there for them. Lamont tells Peter that it sounds like his wife and aunt could teach him about manning up and asks Peter why they would hang him out to dry now. Peter comments that he does not know how much more they can take ("they" meaning him and his family) and tells Lamont that he has no idea what the women in his life have had to endure, what they had to do to survive. Again, there is a brief flashback to when Peter, Harry, Gwen, MJ and Flash Thompson used to go out as a group and how MJ and Gwen used to play them like fiddles and they let them play.

Back at the Coffee Bean, Brady is growing impatient with MJ, as she is refusing to give Peter up, even after he offers her and Aunt May full immunity and reassures her that Peter – once captured – will he kept in a secure location outside of the general populace, super-powered or otherwise. Before MJ can say anything, Brady goes on saying that it is time for the Parker women to put the Spider-Man nightmare behind them and move forward. MJ tells Brady that the nightmare will never end and that he does not have a clue what Peter has lived through, what he has lost and what it has cost him. In another brief flashback, paying tribute to Amazing Spider-Man Volume 1 #87, we are treated to a scene where a feverish Peter Parker reveals to his friends (and Arthur Stacy) his secret about being Spider-Man. As we revisit that scene, Mary Jane continues explaining to Brady that the burden Peter had to carry alone – that is keeping his identity secret for fear of harming his loved ones – was his nightmare, and they were all just living in it.

At Hopper's Dinner, Peter is in total distress, to the point of shedding tears. Despite Peter telling him to arrest him, Lamont is not sure that is what Peter really wants him to do. Peter is so desperate that he suggests that Lamont make an anonymous call to S.H.I.E.L.D. and bring him in. Sitting across from Peter, Lamont pulls Peter's fake moustache off and tells him not to be an idiot and to think of his wife. Peter replies that he always thinks of his wife. He then explains to Lamont that he lost his parents at a young age and ended up being raised by his Aunt May and Uncle Ben, which was pretty much the only good thing that happened to him as a kid. Then there was Mary Jane, which was pretty much the only good thing to happen since. The subsequent death of his Uncle Ben was bad but it's what gets him out of bed every morning. And knowing that MJ is in that bed waiting is the only thing that lets him stop every night.

At the Coffee Bean, MJ tells Brady a story about how this one Christmas, before she and Peter got together, she made him a mix tape to essentially tell him how she felt about him, which was a popular thing to do back then. She wanted Peter to like her back so she asked him to make a tape, in order to find out how he felt about her. That, however, did not turn out as she expected. The tape Peter made did not contain music. It was actually a recording from a half-episode of Nova he taped off PBS and a lecture on magnetic fields, which was his own nerdy way of telling her he was "attracted" to her. The ensuing flashback explains how MJ first reacted to receiving the tape from Peter. She was hard on Peter for not getting her a tape that contained music until she realized that Peter had done exactly what she had asked him to do. She had earlier told him to make a tape of stuff that is important to him, and that's what he had done. As Peter explained this to her, she felt horrible for saying that his tape was boring and stupid. MJ did not hold it against him and proceeded to take a Santa hat out of a bag, telling him that in spite of him being a big nerd, she still got him something for Christmas. Seeing the mistletoe dangle from the hat freaked Peter out and he pretended to have to go somewhere, leaving MJ to stand alone on the sidewalk. Back in the present, Brady tells MJ that she is remarkably spacey for a woman who is facing 20 years in prison for treason; therefore, she should really consider their offer or else. MJ sarcastically asked Brady if he intends to double-arrest her or something like that. Brady tries to scare MJ by implying that bad things happen to girls that look like her in prison but MJ is not easily scared and/or bullied: "My loyalty runs deep you sad little man".

Back at Hopper's Dinner, Peter tells Lamont about the first thing MJ said to him when she first met him, which is the now classic line of "Face it Tiger, you just hit the jackpot!". Peter explains that he could have run away screaming but there was something about Mary Jane that kept him coming back. Peter ponders if perhaps it was the fact that he could not explain her that fascinated him so much. The ensuing flashback is the same as that of the previous ACT, but this time, it is from Peter's point of view. He realizes how big a geek he is when he sees Mary Jane's reaction to the tape he's given her. He also comes to the realization that he really blew it. When MJ pulls the Santa Hat out and puts it on, Peter immediately notices the mistletoe dangling from the end and is too much of a chicken to kiss her, which is why he pretends to have to go somewhere and quickly walks away. Back in present time, Lamont gets a page and it is not good news. Coincidently, Peter also gets a page at the same time. When Lamont gets off his cell phone – having called in to find out what is going on – he tells Peter that the feds have MJ at the Coffee Bean and tells him to go save her and never talk to him again. Peter quickly takes off.

Meanwhile at the Coffee Bean, MJ tells Brady that despite being broke all the time and being on the run constantly, that's her marriage and she would not change it. When she was at her richest, she felt like she was also at her poorest, so to speak. She does not even recall why she and Brady split up all those years ago. All she knows is that it was the worst time. Brady tells MJ that he felt something back then and thought that they could have gone further. MJ replies that one almost hookup does not make them lovers and she is surprised that that's what he thinks they were. She wonders if this is his pathetic attempt at saving her from her big bad life. Having had enough of that conversation, Brady tells MJ that he is tired of playing games and that she is wanted for serious crimes. Either she tells them Peter’s whereabouts, and walks freely, or she is under arrest. MJ does not respond to Brady but she gives him one heck of an evil look. Brady takes a pair of handcuff out and asks her to think about what Peter has done to her life and imagine what he could possibly say that would make this mess she calls life any better. In the ensuing flashback, Peter is about to board a plane to Paris (with Robbie Robertson) and Mary Jane is there to wish him "bon voyage". Before Peter gets on the plane, he finally kisses her for the first time, telling her that he will be back. As he disappears around a corner, MJ replies that she will be waiting (always and forever). Back in present time, MJ puts her wrists out and gets handcuffed. As Brady reads her rights, he notices a small spider-tracer on the seat next to where MJ was sitting down. When Brady asks MJ what it is, MJ replies that she was not rambling, she was stalling, so that Peter could come and save her. Just then, Peter – half dressed in his black costume – comes crashing through the dinner’s window. Before any of the S.H.I.E.L.D. agents can hit their mark, Peter is in and out of the dinner what MJ in his arms.

Peter takes MJ to the Empire State Building – continuing from ACT 1 – and tells her that if she wants to turn herself in, he could hide somewhere and wait for them. And when they would show up, he would give them a good show and slip away. MJ does not want to hear anything about it and tells him that her marriage to him means too much to her and that this is their life, forever and always.