Peter was really getting settled into living with the Avengers; Tony had even designed a new suit based on his Iron Man armour. MJ was getting back into her acting career, and Aunt May was starting a relationship with Jarvis.
However, things soon turned sour, as the government considered installing something called the Superhuman Registration Act. It started to gain strength after Nick Fury enacted an unsanctioned mission into Latveria, believing their prime minister Lucia von Bardas was supplying equipment to several B-list villains.
Peter, unfortunately, was part of this mission, and Lucia von Bardas attacked in retaliation. Nick Fury was blamed for the fiasco but escaped before being arrested. However, he was replaced by Maria Hill, who didn't like the idea of superheroes taking the law into their own hands and wanted them to work for the government.
The House of M incident didn't help either.
MJ was in the kitchen looking at today's Daily Bugle newspaper about the Registration Act.
"So if this bill does get past, what exactly would happen?" MJ asked curiously.
"It would more or less mean that we work for SHIELD," Steve explained. "The idea is that they would get paid and trained to save lives, but we would be limited to what we can do."
"Getting training and getting paid doesn't sound so bad," said MJ.
"Except they would want everyone to reveal their identities to the public," Jess added as she pulled herself a cup of coffee. "That would mean heroes like your husband and Ghost Spider would have to reveal their identity to everyone if they want to continue their hero work."
"Oh," said MJ, realising the extent of this. "Which would put targets on their friends and families."
"Something that the government doesn't seem to understand," Luke grumbled. "That's why your hubby and Tony are in Washington, DC, trying to get this bill rejected."
"I haven't heard from Ghost Spider for a while; she mentioned that she was close and locating our daughter," said MJ, troubled.
"I imagine she's on the run with Nick Fury," Steve assumed.
"Hill more or less demanded that Ghost Spider reveal her identity," said Jess. "When she refused, Hill tried to arrest her; I think she's now on the run."
MJ looked immensely frustrated. "We were so close to finding our daughter."
"I'm sure if this all blows over, you'll have your daughter back in your arms in no time, Mary Jane," Steve assured her.
"She would be a little big; she would be about four years old now," said MJ, looking crestfallen. "And she must really hate us; she probably thinks we abandoned her."
Aunt May then handed her a cup of coffee. "She's a Parker, she'll be strong."
The conference at the White House was interrupted when Titanium Man attacked, but Tony and Pete saved the congresspeople in their costumes. As a result, the people second think about the Registration Act.
However, a terrifying incident occurred. A group of young heroes named the New Warriors decided to make their crime-fighting exploits into a TV show. During one of these episodes, they cornered a bunch of villains in Stamford, but one of them, Nitro, used his powers to create a devastating explosion, demolishing a number of buildings, including an elementary school, on a school day.
Over 600 civilians perished, 60 of them were children, and it sent massive shockwaves to the country. Hatred for heroes spread across the country, and some people even attacked Johnny Storm; he was beaten so badly that he ended up in a coma.
The Superhuman Registration Act was passed, but it also split the human community. Captain America disagreed with the Registration Act, feeling that it violated the free world of good men and women trying to save lives, but after the incident at Stamford, Tony decided to side with the government.
"So, Cap is on the run," said Peter.
"Director Hill gave him a direct order, but he refused," said Tony regretfully. "Luke and Daredevil are also on the run."
"Both Scarlet Spider and Ghost Spider are on the run as well," said Peter.
Tony looked at him curiously. "And what about you, Pete? Are you going to join Steve's fight against the government?"
Peter was completely uncertain. "I don't know. The tragedy at Stamford was devastating, and there's no denying it could have been avoided. However, don't you think this Registration Act is a bit rushed? There are hardly any safeguards in it. I mean, you either join the government, retire or go to jail."
"Pete, everyone in the country is angry at the moment, and I can't say I blame them," said Tony sympathetically. "Steve and the others just don't see the big picture. Both Hank and Reed agree with me, and you know how smart they are."
"But revealing identities," said Peter uncertainly. "You'll be all right for you. You're multibillion, and you don't have any extended family. However, it's different for me."
"But if you join the government, your family will be well provided for and protected," Tony promised.
"I'm going to have to discuss it with them before I make a decision," said Pete.
"I understand, but Peter, you need to make a decision soon. Hill is already getting on my back on the other non-registered heroes, and they don't know they live under my roof."
Peter discussed this with Aunt May and MJ, and they convinced him it was the right thing to do. So, with their support and Tony's assurance, he revealed his identity to the world on live television, which had several mixed responses.
Jonah was particularly vocal and tried to sue him for all the money he took while working for him. One of his ex-girlfriends, Deb Whitman, was so furious that she began writing a book about it. However, the thing that really hurt him was Liz, who began blaming him for all the misfortune in her life.
Gwen was currently with Ben in a secret hideout with Captain America and his Avengers. They had just watched the live broadcast.
"I can't believe he actually did it," said Ben.
"In his defence, he does have his family to think about, but he looks up to Tony as a sort of mentor," said Gwen.
"You really think you can go along with this?" Ben asked.
"Pete has a strong moral compass. I'm sure he'll start to see the dark side of Tony and his Avengers soon enough," Gwen assured him.
"He does which side will welcome him, but until he does, he is the enemy," said Steve, approaching the two of them. "Right now, Tony is starting to arrest all the superheroes who refuse to register, and we need to figure out where they're taking them."
"There's not a lot of us, Cap," Ben pointed out. "Not to mention, got a few heavy hitters on their side."
"We'll work with what we have, but I need to know if I can count the two of you?" said Steve.
"You can count on us, Cap," Gwen assured him.
Steve nodded. "I really do appreciate this."
MJ was currently in the living room at Avengers Tower, talking to her sister on the phone.
"When I saw the news, I couldn't believe my eyes," said Gayle. "Peter is Spider-Man?! You're married to Spider-Man?!"
"Sure am," MJ smiled.
"And now you're telling me that you're living with the Avengers," said Gayle in disbelief.
"Pretty much."
"Mary, you sure do live dangerously."
"This isn't going to be a problem, is it?" MJ asked concerningly.
"I don't have a problem with Spider-Man, and I neither do the boys; in fact, they're bragging to their friends that their uncle is a superhero," said Gayle with a small chuckle. "I am, however, concerned about you. Now that Peter's identity is out in the open, all the enemies are going to come after you."
"Don't worry about it, sis; I'm perfectly safe," MJ assured her.
"Mary, I'm not even sure if you know the meaning of the word. Given what Norman Osborn did to the two of you when he found out Peter's identity. I doubt the Avengers would be able to protect you all the time, and as for the government, they are too busy hunting down heroes to deal with the villains."
MJ paused as Gayle made a valid point. "Gayle, I'll be fine."
"Well, due warning, Dad isn't particularly happy about the situation, and you know that he's never been fond of Peter," Gayle warned. "And you really should consider what you're going to do if you don't have the protection of the Avengers or the government."
MJ didn't take Gayle's words seriously, but things started to change. Tony had arranged an ambush for Steve but ended up in a fight. Then, Tony and Reed unleashed a cyborg Thor onto the battlefield, but something went badly wrong.
The cyborg accidentally killed Goliath, who was fighting on the resistance side. Peter was utterly devastated by this, and so were a number of heroes who began to think that Steve was right. Sue Richards had already switched sides, and others soon began to follow.
Peter was willing to give Tony the benefit of the doubt, but all that changed when Tony revealed the prison cells they had created for unregistered heroes. It was located deep in the Negative Zone, and they had just thrown every unregistered hero in there without so much as a trial, waiting until they agreed to the terms given to them.
Peter soon shares his concerns with MJ.
"It's just not right," said Peter, looking at her. "These are men and women who risk their lives to save people are now being treated like criminals."
"Wasn't this the outcome we all anticipated?" MJ frowned.
"I assumed they would at least get a trial or some sort of sentence, but now they're just locking them up and throwing away the key," said Peter, shaking his head. "How can I go out there and apprehend former friends, knowing that they're never going to see the light of day again."
MJ could see that Peter was really conflicted. "What are you going to do?"
Peter looked at her. "I honestly don't know, but I won't do anything unless I have the support of both you and Aunt May."
MJ grasped his hand and looked into his eyes. "Peter, whatever you decide to do, we'll support you all the way."
Peter smiled and hugged her, knowing what he had to do.
That same night, Peter begins to leave the tower with both MJ and Aunt May, but he knows he can't leave them behind. They could be used as hostages. Unfortunately, his defection was not unnoticed, and soon, Tony was blocking his way in his armour.
"I'll admit I'm disappointed; I had hoped that you would see reason," said Tony regretfully.
"You're locking people up for trying to do good," Peter argued.
"They're breaking the law, but you're doing it right now," said Tony. "Peter, if you turn around right now, we can forget the entire thing."
"No," said Peter, clenching his fist and activating his armour. "I won't stand here and let you lock people up without a trial!"
Tony sighed. "I had hoped I never had to do this."
He then pulled his visor down and activated an override that he had inputted in Peter's armour. However, to his surprise, Peter suddenly launched forward and punched him hard in the face, causing him to crash into the wall.
"Did you really think I wouldn't have noticed this armour's override and tracking system?" Peter snapped. "You knew I would turn on you if I found out the truth; you never trusted me."
Tony was rather surprised that Peter managed to override his override. "Given the fact that you're defecting, it seems as if I had every reason not to trust you."
"Actually, that's the reason why defecting," Peter countered. "I mean, how can I trust the leader? Who doesn't trust the men he leads?"
Peter then instantly webbed Tony up and made his getaway.
Unfortunately, his defection did not sit well with Hill, who sent the Thunderbolts after him. The Thunderbolts were a group of pro-registered villains; after the heroes' mass defection after the ambush, SHIELD decided to recruit villains into its ranks.
Tony had been strongly against this, but Hill overrode him. Peter had managed to make his way to the sewers, but he was then ambushed by Jester and Jack-O'-Lantern, who beat him up to near death. They probably would have killed him if Frank Castle, a.k.a. the Punisher, hadn't intervened and saved him.
Castle was then brought into the secret hideout of the Secret Avengers, who nursed him back to health. Dr Foster, a friend of Thor, was the Secret Avengers medical officer who managed to save him. As he lay there in bed, both Gwen and Ben accompanied him.
"Sorry I didn't join up with you guys soon," said Peter regretfully.
"It's no problem, Peter; you had your family to look out for," said Gwen.
"Speaking of which, where are they?" Ben asked.
"They're in hiding at the moment," said Peter. "I don't think they'll be in any real harm; after all, it's me that the government is after, but I would appreciate it if someone could get them to safety."
"Don't worry, we'll handle it," Gwen promised. "But it seems the government is more desperate than we thought if they're recruiting villains."
"I'm surprised Tony would consent to this," Ben frowned.
"I don't think he has much choice in the matter," said Steve as he entered the room. "He's no longer calling the shots, despite what he might think."
"He is still making some decisions," said Peter.
He then began to tell them about the superhero prison in the Negative Zone.
"Stark has gone too far!" said Steve, clenching his fist. "Does he not realise what he's doing?"
"Maybe we told the public," Peter suggested.
"I doubt they'll be sympathetic," said Gwen. "Given what happened with Nitro in the New Warriors, they'll feel relieved that these dangerous superpowered individuals are locked up."
"So what do we do?" Peter asked.
"We come up with a plan," said Steve.
Peter was soon reunited with both his wife and Aunt May, who were relieved to see that he was alive.
"Peter, I was so worried," said MJ, hugging him tightly.
"I'm fine, MJ," Peter assured her.
"From what Ghost Spider told us, you nearly die if it wasn't for the Punisher," said Aunt May sternly.
"It was a close call," Peter admitted.
"What are you going to do now?" MJ asked.
"Steve wants us to rescue all the heroes that are imprisoned, so he's coming up with a plan," Peter explained. "And I'll no doubt be playing a part in it."
"Just be careful," said MJ.
"I promise."
The final battle of the Civil War soon began, and they managed to infiltrate the Baxter Building with a little help from Castle. However, after he gunned down a few villains who wanted to join them, he was immediately kicked out of the Secret Avengers.
Sue had gone to Atlantis to convince Namor to join their side, but to no avail, and the X-Men chose to remain neutral as well. Apparently, after the House of M incident, Cyclops felt as if humankind had suffered enough. However, Black Panther and Storm, who had just recently married one another, joined, so there was some good news.
They managed to get into 42 without incident, but they encountered Tony and his Avengers when they got inside. As it turned out, they had a spy in their midst, but to Tony's astonishment, so did they, as Hulking had disguised himself as Yellowjacket.
Cloak then created a portal and sucked everyone out of the Negative Zone and back into New York City. Once there, a massive fight began to rage through the streets, causing massive damage; you got even more complicated when Namor and his army joined the fight on the side of Captain America.
As the battle raged on, it looked as though the Secret Avengers were winning, but just before Steve dealt the final blow to Tony, he was instantly pulled away by cops, EMTs and firefighters. It was then that he realised the full scope of the damage caused by this conflict, and to avoid bloodshed, he surrendered.
Steve also insisted that he would be the only one to be punished and that the other Secret Avengers should be given amnesty, to which the government agreed. So, the civil war came to an end, but not everyone was sure if it was for the best outcome.
Peter himself was now stuck in limbo, and with his identity now revealed to the world, neither he nor MJ could get a job. He was also reluctant to ask Tony for help; it was more or less all his fault that they were in this mess.
Additionally, since they can no longer live at Avengers Tower and Aunt May's house hasn't been rebuilt, they have nowhere to live. They can now only live on Aunt May's pension, and the only place they could rent was a shabby hotel room.
On the plus side, Peter was no longer being hunted by the government, so they didn't have to run for their lives anymore. On the negative side, now that his identity was public, he was the victim of the paparazzi.
Even though it was dangerous, Peter had to see Harry, who was still in a coma. He went to the private hospital where Harry was located, making sure to get in through the window, and when the coast was clear, he went to visit.
"Sorry I can't visit you soon, Harry," Peter sighed. "The whole mess with the civil war prevented me from doing so. The entire world knows my identity, but now I'm completely out of the job, as is MJ. I really messed up our lives."
He then suddenly heard a gasp and quickly turned around and saw Liz standing there.
"Uh, Liz, I," said Peter, unable to find the right words. "I better get going."
He was about to make his way to the window when he suddenly felt a hand on his shoulder. He slowly turned around to look at Liz.
"Peter, stop," she said. "I owe you an apology."
"You do?" Peter blinked.
"I blamed you for all the misfortune that happened to me, but it really wasn't your fault," she sighed. "You're hardly to blame for what happened to Mark. Plus, if anyone is really to blame for messing up our lives, it's Norman Osborn."
Peter nodded. "Yeah, even before he became the Green Goblin."
"That said, I don't think you should see Normie any more," she said. "He still blames Spider-Man for what happened with his father; he was just too young to understand what was going on and still is."
Peter then looked at Harry and then back to Liz. "If he does wake up, what's going to happen between the two of you?"
Liz sighed as she looked at Harry. "I honestly don't know. I know he wasn't himself, but he still endangers our son and himself. I want our son to be as far away from the Norman legacy as possible. Do you know that he buys Spider-Man dolls just so he can take their heads off?"
"That's a little disturbing," said Peter, fighting the urge to rub his hand around his neck.
"It's not healthy for a child his age; I only hope he grows out of it. However, for that to happen, he must stay far away from Spider-Man and the Green Goblin."
Peter nodded. "I understand; I'm just sorry we've come to this."
Liz nodded. "So am I."
With the civil war over, Gwen continued to track down little May. Unfortunately, the damage done to the city caused many people to relocate, making it harder for her to track one little girl. She could only hope that she could find hope soon because, from the memory she had, both Peter and MJ were getting to the point where they split up.
Of course, those memories were from an alternate timeline which no longer existed. However, most of her memories have been mostly accurate so far despite the alterations, and with Peter's identity now public, it is easier for villains to take a shot at him or his family.
She then swung over to where Peter was staying at the moment to give him the news and think about where they would go from here. That's when she saw someone on the rooftop of the opposite building aiming a sniper rifle at the window of Peter's room.
Realising what was about to happen quickly swung down and attacked the sniper. She fired some webbing at the rifle and pulled it up just as he pulled the trigger and then knocked him out. However, she then heard screams coming from Peter's room, much to her horror.
We're getting to the point where things start to change, and while I'll try to stick to the comics, I will be adding my own stories as well. I just hope that in the comics, Spider-Man gets his happy ending.