Disclaimer: I do not own these characters, they are the property of their creators, nor am I seeking to make a profit from this.
After that day, things slowly started to return to normal, if one considered all the Avengers moving into their respective apartments in Stark Tower "normal." The entire ordeal had brought them closer in a way that they would never really be able to understand, or quite explain. Clint figured it was just the fact that when you have bath time together and once you wake up in the middle of the night covered in vomit, things can never be quite the same.
Clint and Natasha moved into the apartment that Tony had designed for Clint on the penultimate floor - nice and high for Clint.
They went back to work, going on periodic missions; sometimes alone, but most of the time together.
Two weeks after Thor and Loki returned to Asgard, Natasha and Clint got a call from Fury saying that Sarah and James Bates had both been sentenced to life in prison for aiding and abetting in slave trade.
Natasha talked to Peter a few times, and he told her that Deadpool was actually hilarious to work with, sometimes scary, but mostly good. "He's an incredible fighter," Peter had told her the last time they had spoken. "I'm actually learning a lot from him, and he makes work unpredictable and pretty fun."
Clint and Natasha continued to get closer; once they had more alone time together they had the chance to talk about the past few months. And when one of the drawings that Loki had done while he was at SHIELD, the one with Loki and Natasha ended up on the refrigerator either mentioned it.
They did talk about kids, briefly, one afternoon. They were both sat at the kitchen table, Natasha was drinking tea while Clint read over his mission report once more before he turned it in.
"Clint," she said, and he looked up from his papers. "Do you think we would make good parents?" Clint sat back in his chair and looked at her curiously.
"I think we did." He smiled at her, and she grinned back.
One month after their return to Asgard, Thor and Loki came back. It was a Saturday and everyone was lounging in Tony's apartment having a lazy day, as it was freezing cold and snowing outside. Thor, once again in typical Asgardian garb, banged the door open.
"Hello, my friends!" He boomed. Natasha had been leaning against Clint watching the news with the rest of her teammates, but at the sudden noise of the door opening she had started and was half standing, half kneeling on the couch. The others had swerved around. "Hey Thor!" Tony called, "Come on in."
Thor entered and revealed Loki standing behind him. Natasha relaxed and she stood looking at the man she had grown so fond of. She didn't know how to describe her feelings for the man - she cared for him, but at the same time she didn't really know him. She knew how he was as a child, but not how he was as a rationally functioning adult.
He looked healthy, which told her that he hadn't been languishing in a prison cell the past month. He looked calm, as he always had when he had been a child. His hair was back to its usual slicked back style, as opposed to the soft black mess of hair that went everywhere when he was a three-year-old.
"Hello Loki," she said, the first to address him.
"Hello, Natasha Romanoff," He replied. "If you do not mind, I wish to speak to you and Clint Barton alone." Natasha blinked, looked down at Clint, who shrugged. Clint stood and together they walked around the couch and joined Loki in the hallway.
"How have you been?" Natasha asked after a few moments.
"I have been well. When I regained consciousness in Asgard I was sentenced to certain. . . magical restrictions, so I am no threat to Asgard or its allies. What I wanted to say. . ." He hesitated, his brow slightly furrowed, as if he didn't quite know how to say what was on his mind. "I wanted to say thank you."
Natasha's face softened. So he has changed.
"You could very well have left me at SHIELD in the beginning, and not bothered with me, but you treated me like one of your own and for that I am eternally in your debt. I have had much time to dwell on all that happened here, and your kindness will forever stay with me." Loki stopped, and closed his eyes before leveling his gaze on Natasha.
"And thank you for saving me after I was taken by the slavers."
"You're welcome," Natasha replied.
"No problem," Clint said, "Just don't try to take over earth again anytime soon."
Loki laughed softly, "No, I do not think I will." He smiled.
They did not stay for long after that. Thor claimed that the real reason they had come was because Loki still hadn't removed the helmet from the Statue of Liberty. Loki went up to the roof with Thor, and the others stayed inside, settling back down to enjoy the rest of their Saturday together.
Natasha looked out the window and across the city. Through the snow and gray skies she could just barely see the darkened horns on top of the Statue of Liberty dissolve and disappear. She turned her attention to Tony and Steve, who were arguing once again, a smile on her face.
I hope everyone enjoyed this story, and I'm sorry it took so long to get the epilogue out.
EDIT 1/1/13: There's now a series of one-shots that take place during this story up, called "Bringing Up Babies".