The Visitor/Time Displaced Daughter arc
First of all Peter would reveal that he is Spider Man to his closest family and friends (such as Aunt May and Harry, Flash Thompson if he doesn’t know). Peter is creating a new suit which materializes from a badge like device attached to his person which allows him to turn from Spider Man to Peter Parker in an instant and the device can also house other clothing styles. His new suit enhances his current power set with an emphasis on his Spider Sense, gives him Enhanced Vision, Camouflage capability and even Venom Blasts. While testing his new suit around New York, Spider Man spots Annie May Parker from the Renew Your Vows storyline. She is injured and bleeding atop rooftop. Spider Man takes her to a Parker Industries Medical Facility where she is healed. He learns that she is the daughter of Peter Parker and Mary Jane from an alternate universe. Spider Man discovers a new use of his Spider Sense allowing him to connect his mind to Annie’s via their mutual Spider Sense ability to get a better understanding of who Annie is, her history and how she got from her universe to his. Annie tells Peter that her parents sacrificed themselves to save her from their certain death scenario back in her universe and she was transported through a portal. Peter comforts the saddened child and upon embracing her, a fatherly instinct awakens within him driving him to tell Annie that he will protect her, care for her, train her to better use her powers and if possible bring her parents back and restore her life.
With that said, Peter uses his resources to have her registered as a citizen and then adopted. Peter introduces Annie to Aunt May and the older woman is surprised but noticeably happy about her new granddaughter (or grandniece in this case). Annie sees a picture of Mary Jane and begins to remember her own mother (MJ from her own universe) causing her to be sad. Peter explains to her why he and MJ are not together in this universe and that despite how hard it must be for her, she cannot expect Mary Jane (Earth 616) to be something she is not. Peter Parker also publicly acknowledges Annie May Parker as her adopted daughter in a Parker Industries announcement. The duo go on several adventures together as Spider Man and Amp (Annie’s superhero identity) developing a deep father daughter bond and dependence for one another.
One day after thwarting a villain’s warpath, Peter and Annie arrive at a lunch date with Harry, Betty Brant and Flash Thompson (having returned from space) only to also encounter Mary Jane. Mary Jane “tigers” Peter and then proceeds to introduce herself to Annie and complement her on her looks and red hair (MJ learned of Annie through the media). Annie is stunned and begins to remember her mom, her own Mary Jane and at the same time remembers what Peter told him about MJ. She hides behind Peter trying to contain her tears. When MJ asks about her, Peter talks to her in private and explains that she is the daughter of Peter Parker and Mary Jane from an alternate universe and how she ended up with him. MJ is surprised at this revelation. Peter tells her that he has no right to ask this of her but nonetheless he asks her if she would let Annie pretend that she is her mother to calm her down and to help her deal with her traumatic situation. After the lunch date is over, MJ talks with Annie about her predicament and lets the time displaced girl pretend that she’s her mother. Annie hugs MJ calling her mom and telling her that she misses her so much. MJ feels a motherly instinct awakening inside of her afterwards. This encounter sets up a chain of events which see Peter and MJ reconnecting. Annie becomes an important part of Peter's world and cares for her immensely. He restlessly continues to research ways of bringing back a universe since he cannot contact Reed Richards. Tragedy strikes Peter when Aunt May dies in a car accident. Peter is devastated but he confesses that he had always been prepared for when she might die. Harry, Mary Jane, Jameson, Flash, Liz Allen, Betty Brant and several others were present at the funeral. Her death also broke the deal they made with Mephisto but reality was not altered. Instead Peter and Mary Jane began to remember their married life and forgotten love.
The Last Superhero arc
A storyline unfolds in which every superhero in the world have mysteriously vanished. All except for Spider Man. Spider Man tries to contact other heroes to no avail. He stops by SHIELD to see if Director Hill has heard from any of the heroes and she confirms that all of the teams and individual heroes they keep track of have vanished without a trace. In Times Square, Spider Man faces off against a Hulk Clone whom he defeats thanks to his new upgrades. Spider Man calls Mary Jane to see if Tony Stark is still active but she tells him that Stark’s whereabouts are unknown and its beginning to worry her. Spider Man drops by Stark Tower to request Mary Jane’s help and after FRIDAY confirms that she has lost communication with Iron Man, he turns on the news revealing the official news that every superhero and every team have vanished leaving Spider Man as the planet’s sole superhero. Following this newscast, villain attacks occur around the world resulting in absolute chaos (the reality is that the superheroes were part of a rapture by a cosmic entity and are fighting to save the universe). Peter puts the resources of Parker Industries to work against this rising chaos and works with SHIELD and other agencies to secure the world. He enlists Mary Jane’s help as he goes on to stop the most dangerous villains. She acts as his eyes, ears and source of information and helps Peter take down many villains. Peter has Mary Jane tell FRIDAY to deploy Iron Man armors around the world to maintain security. After globetrotting, Peter returned to Stark Tower to Mary Jane where things have become worse. Peter senses Annie in danger and rushes off to save her at her school from Beetle and brings her back to Stark Tower. Mary Jane continues to help Peter take out villains in New York and begins to take a liking to it since she is helping Peter fight crime but without having to suit up. After locking away numerous villains, Spider Man notices that most of his own villains are yet to be found.
Suddenly, the Green Goblin emerges with most of Spider Man’s villains under his command in a broadcast in New York. He claims that he will turn New York City into his personal playground. Spider Man takes Mary Jane and Annie with him to the Baxter Building where Harry and Anna Marconi are waiting for them. Peter has the entire city evacuate before the Goblin’s plan comes into fruition along. Peter has FRIDAY take over as his support while makes sure that Harry, MJ and Annie are with the evacuation. Spider Man and his Iron Man armor supports go on to hunt down the Goblin and his many foes but is lured into Times Square where his enemies converge on him. The Goblin’s plan comes into fruition and New York is made into a prison and Spider Man is alone against many of his foes. Among them are Carnage, the Vulture, Scorpion, Electro, Mysterio, Rhino, Shocker, Lizard, Sandman, Kraven, Molten Man, Hydro Man, Hobgoblin, etc. The Goblin broadcasts this across the world as Spider Man battles to survive. Spider Man’s upgrades and experience allow him to stand a chance against so many foes keeping in mind that he has to protect MJ and Annie. Suddenly the heroes who disappeared reemerge and collectively try to penetrate the barrier around New York City to come to Spider Man’s aid. Spider Man begins to tire and takes many attacks from his enemies. Annie sees this and runs off to her father. MJ follows her as well as Harry. When Annie and MJ arrive to aid an injured Spider Man, Goblin attempts to kill them by ramming them through his glider. For all the world to see, Spider Man stops the glider even though he is impaled by it and his blood is spilled over MJ and Annie. Spider Man destroys the glider and knocks back the Goblin before losing consciousness. With everyone believing Spider Man to be dead, the heroes filled with rage break through the barrier and help take back the city surrounding Spider Man’s villains. Annie and MJ are beside Spider Man hysterically begging him to not die. Spider Man moves slowly and manages to stand up to the awe of Annie, MJ, the heroes and the villains. In his grievously injured state Spider Man unleashes his full fury and defeats the Green Goblin while the rest of the heroes defeat the remainder of his villains. The Goblin attempts one last strike against his archenemy but Harry kills him telling Peter that it was his responsibility to stop his father.
One More Time Again arc
Despite the victory, Spider Man is severely injured and near death. This brings Peter’s friends and loved ones together at his side in the hospital bed. Peter avoids death and he begins to heal though it will take some time and a caretaker. MJ volunteers to oversee his recuperation. In his time off from being Spider Man, Peter focuses on running his company, being a father to Annie and researching ways to bring back Annie’s real parents. With the help of a Cosmic Cube and Spider Man 2099, Peter successfully restores Annie’s home universe and builds a portal in the Baxter Building. He and Annie walk through the portal but unknown to them, Mary Jane had come to visit and followed them through. Annie is then reunited with her parents, the alternate versions of Peter Parker and MJ. Mary Jane walks in and both Peter and Annie are surprised. In that moment Peter and Mary Jane meet their counterparts who are Annie’s parents. The two MJ’s get to talking and MJ (from Earth 616) asks her counterpart about her life with Peter and how she managed to stay with Peter and have a child despite all the danger and complications. The alternate MJ explains that she and Peter were always meant to be together, that any life made without him in it would be incomplete and speaks from experience when she tried to build a life away from him. Through willpower, resolve and their love, the alternate MJ and Peter have overcome all challenges to their marriage and their family emerging the stronger for it with MJ so used to villains’ attacks that she herself can take on her husband’s foes. The alternate MJ correctly guesses that MJ and Peter still hold deep love for one another and encourages her to rekindle her relationship with him and to not make excuses about danger and complications, that together they will overcome anything. The real MJ explains to her counterpart that she wants to live her own life and not have it consumed by Peter and Spider Man. The other MJ tells her to do it, to do what she wants to do but no matter what, her path and Peter’s will always meet. Peter and MJ watch as Annie departs with her parents through the portal though not before Annie hugs the two, telling them that she loves them. She gives Peter a locket with a picture of her and him in an amusement park and with Spider Man and Amp on the other side and promises to visit if she can.
Sometime after Annie’s departure, Peter laments the loss of her adopted daughter and Mary Jane contemplates about the words of her counterpart. Despite both of them having achieved stability in their separate lives, the two feel a longing in their hearts, an empty void that swallows them whole. In addition to that, the memories of their forgotten past as a married couple continue to surface further deepening their desire to be with each other. After reflecting on his recent experiences and his entire life, Peter achieves clarity and realizes what matters most to him in the world. One day, Mary Jane is walking back to her home when it gets cloudy and she rushes her pace. Peter Parker as Spider Man waits for Mary Jane outside her home hanging upside down in his webbing. When Mary Jane is at her door, Spider Man descends and makes his presence known. The two friends and former lovers are in each other’s presence, alone for the first time in what feels like long time.
Mary Jane: Peter! What are you doing here?
Peter: (slight silence) I wanted to come… to see you and to talk to you, because it feels like a long time since we’ve done that…
Mary Jane: What is it?
Peter: (slight silence) How are you?
Mary Jane: What?!
Peter: How are you really?
Mary Jane: Alright I guess. What’s this about?
Peter: Did you do it? Did you build the life you wanted for yourself?
Mary Jane: (slight silence) Yes… I think I have.
Peter: Are you happy?
Mary Jane: Peter… why are you here?
Mary Jane: Why are you asking these things?
Peter: (slight silence) I just needed to, because… I’ve realized what’s important to me in this life. And it’s not Spider Man, it’s not my power or responsibility, it’s not even my friends and family. Gwen Stacy is not the love of my life, and Aunt May is not the most important person in the world to me.
Peter: It’s you. Just you.
Mary Jane: (slight nervous silence) Peter… we’ve…
Peter: My double life has been a nightmare for you, I know that. You want to live your life the way you want to and with whoever you want to. I admire you for it and respect your choices.
Peter: You and I, we’ve, had a turbulent relationship. Despite that, we fell in love and found happiness with each other. And I will never forget it, neither the good nor the bad. Those are my most valued memories.
Peter: To my core I’m still the same. I haven’t changed. But you… you moved on, and encouraged me to do the same, to find happiness and live.
Peter: And I’ve tried to, I’ve tried to move on, I’ve tried to go on living for my sake, to let go of you. Believe me, I’ve tried.
Peter: But I can’t. Because I don’t want to. I don’t want to move on from you. I don’t want to be with someone that isn’t you.
Peter: You are always in my mind. The simple thought of you gives me the strength to turn a losing battle into a resounding victory in every aspect of my life. You are the force that drives me forward, you are what I fight to protect, you are my definition of happiness, and you are my heart, my soul… my life.
Mary Jane: (Mary Jane stays silent, hanging on Peter’s next words)
Peter: I will always watch out for you and gladly risk my life for yours without a thought, without regret. Whether you’re with me or not, whether you’re near me or far away, whether our lives take us in different paths and make us distant… I will always be there when you need me the most.
Peter: Whatever trouble you find yourself in, whatever villainous plot you’re in at the hands of Green Goblin, Venom or some other foe, whatever your need, I will save you. Because you are the only one that’s important, the only one relevant in my existence. No one else matters. No one will ever replace you in my life and I will never care for anyone more than you.
Peter: If you choose to leave us behind, to give up on us permanently, to live out your life alone or with whoever you want, that’s alright, because it won’t change the way I feel about you and what I’m willing to do for you.
Peter: No matter what deals we make with devils, what gods we pray to when we’re afraid, what villains get between us or if destiny itself interferes, in life and death…
Peter: Above everyone and everything, Mary Jane Watson… I will always love you.
Mary Jane: (silent, shocked, in tears and with her entire world revolving, Mary Jane is speechless)
Peter: That’s what I came by to say… I’ll never say goodbye again Mary Jane.
Peter: Instead… I’ll see you later. (Peter prepares to leave)
There are several outcomes to this heart throbbing confession on the part of Peter Parker to Mary Jane.
1- The first would be that silence prevails between both of them and Peter leaves after saying farewells to his reason for living. Mary Jane would remain in place processing what she heard and reflecting upon it but with no immediate response or decision. Mary Jane enters her home and begins to shed tears and after recent events which saw her and Peter reconnect coupled with his confession, she struggles for clarity in what she must do, because she still loves Peter and wants to be with him but something is holding her back, mainly the reason why she doesn’t remember her marriage to Peter. After several days, Mary Jane stands outside Peter’s home in the rain. Peter sees her and rushes out to her. He hears her own confession, how he loves him and wants to be with him but is still uncertain. She wants to be with Peter but she doesn’t want to be consumed. Peter reassures her, convincing her that he won’t let her regret it if she finally wants to take the chance to be with him for good. The two are under the rain holding each other when both of them fully remember the past that Mephisto erased and Mary Jane whispers “Alright”. Peter brings her inside and after drying up, they sit together holding each other and finding comfort together reminiscing about their shared history. MJ remembers that she left Peter because she didn’t want to be entangled in Peter’s double life but realizes that it was an excuse for not being strong enough to be with him and overcome their challenges. She’s left Peter numerous times but she always comes back. When she left Peter and lived her own life she still found herself in the middle of battles between heroes and villains and realized that both would never cease to be. Peter and MJ realize they love each other and that they were meant to be together. The two stay together forever and ever.
2- The second outcome (and my favorite) would be that as Peter prepares to leave, Mary Jane puts her hands in Peter’s head and holds him, pressing her face to his in loving affection. She begins to pull down his mask slowly and they have their trademark upside down kiss, intense and passionate, probably the best kiss of their lives.
a. This outcome ends with either Peter departing after the kiss or…
b. With Mary Jane pulling Peter down and taking him to her home for a passionate night. They figure out a way to live with each other for better or worse but with the fierce determination to fight for their love and their life together.