Spoilers for AoU! I was writing a Tumblr post on this topic, and my headcanon kind of got out hand. This was the result. Enjoy and review if you feel like it!
If you want to see the post, check it out on my Tumblr, lilacs-in-the-winter-night.
It's a few days before Christmas, and Clint's leaving the Avengers Tower.
It happened every holiday. At first, no one noticed. Clint always had an excuse on hand: his friend was sick, he needed a new bow, his ex was in town and he wanted to avoid her, he hadn't slept in a week because of Bruce's snoring and he needed a few nights on his own of good rest. No one took the last one seriously, as Bruce's room was three floors above Clint's, but the rest were all easily accepted. They all took days off, after all. No one questioned it until, after a mission, Natasha made a comment comparing the criminal's taste in clothing to Tony's taste in Christmas decorations. Clint said he hadn't seen the decorations; he'd been gone for the week of Christmas when they had been up. Later, Steve made a reference to Thor's behavior at the team's Thanksgiving dinner (Thor had been under the impression that Thanksgiving was similar to an Asgardian holiday that required feasting all night), and Clint gave him a blank look; he hadn't been there either. Tony, thinking about both these exchanges, realized that Clint hadn't been to a single one of the Avenger holiday parties.
He mentioned the conveniently timed absences to Bruce, who opened his mouth to mention at least one party Clint's been at before realizing that Tony was right. He shrugged, and called it a coincidence.
After two years of holidays, Clint started to run out of believable excuses. By then, the others had noticed that he never seemed to be present at the parties either, and his reasons for being gone were met with raised eyebrows and skeptic expressions from everyone but Natasha, who offered no response to them. Eventually, he stopped even giving excuses. A few nights before any major holiday he'd simply leave, and he'd reappear a few days later. No one bothered to question it any more.
Except for Tony. Being in the dark about things really wasn't Tony's style. It drove him crazy that he didn't know where Clint was going, so he decided to make it his job to find out. Unfortunately for him, Clint didn't make the job easy.
He tried the obvious first: when Clint returned to the tower a few days after Easter, Tony asked him where he'd been. No response. A week before Memorial Day, he embedded a tiny tracker chip into the duffle bag Clint always took with him. Clint borrowed a bag from Steve, claiming his own had a hole in it. Before the Fourth of July, he snuck into Clint's room during the day and attached a tracker to Clint's shoe. An hour after Clint left Tony turned on the signal. It led to a trash can about a mile away from the tower. Labor Day weekend he hacked government satellites to see if he could spot Clint from the skies. He couldn't track him down. Thanksgiving he asked Rhodey to follow Clint; Clint left in the middle of the night Monday instead of Tuesday morning like he said he was going to, so Rhodey arrived too late to track him.
So now it's Christmas, and Tony is determined to get to the bottom of this, even if he has to follow Clint himself. It's a cloudy night, and he thinks if he stays up high enough in the clouds, the suit's tracking system can stay locked on Clint and he can stay out of sight. He has Jarvis on constant alert with orders to wake him up if Clint so much as sets foot out of his room. When Jarvis's polished voice lets him know that Clint is leaving, he's up on the roof in a few minutes with his Iron Man suit waiting for him.
He realizes after a moment that he isn't alone. Natasha's sitting at the edge of the roof, watching him. He doesn't know what she's doing there and to be honest, he doesn't really care. He's about to call the suit to him when Natasha gets up and walks over to him, standing between him and the armor.
"You don't need to go anywhere tonight," she says in the cool way of hers.
"Actually, I do," he replies. "Mind getting out of the way?".
"I don't think so," she says, crossing her arms. It suddenly dawns on Tony that maybe Clint had someone who was helping to keep him in the dark.
"You're the one who's been telling Clint about my tracking attempts". It actually made a lot of sense. Tony had tried to keep what he was doing as quiet as possible, but it seemed like very few things happened in the tower that Natasha didn't at least have vague knowledge of. She smiles slightly.
"Took you long enough to realize it". Tony opens his mouth to make some retort, some snide comment, but she cuts him off.
"We all have our secrets Tony. Where Clint goes off to is his own business".
"Yeah, well, I'm not really good at respecting boundaries". The smile slides off her face, and he's almost a little scared about how serious she looks.
"Some secrets are kept for a reason. Sometimes they're kept to protect people. Sometimes you shouldn't push them".
"I-"
"You're not going to find out where Clint's going, and you need to stop trying to find out. Next time, I won't be so nice when I tell you to stop. Jarvis," she calls out to the AI, "Put the armor back in storage. Mr. Stark won't be needing it tonight".
"Of course, Miss Romanoff". Tony may be the one who created Jarvis, but even the computer knows better than to go against Natasha Romanoff.
"After you," she says, gesturing to the elevator, following as he enters it. The floor with her room is higher than the floor with his, so she leaves the lift first. She turns around as the doors are closing.
"Don't try this again Tony. Some secrets are meant to stay that way". The doors slide shut on her last words, and the elevator continues its journey down with Natasha's last phrase ringing inside it.
It takes a lot to discourage Tony Stark once he gets started on an idea. As Pepper's told him, he's stubborn, arrogant, and self-absorbed: none of which are characteristics that lend themselves to giving up easily. He tends to believe he's right, and he's not likely to set aside his plans for the convenience of others. Natasha's words might just have convinced him, however.
It wasn't just what she said. It was the look in her eyes that told him she wasn't messing around. It was the tone of hardness that came from the knowledge of far too many secrets with the potential to hurt far too many people. It was the the vague details he'd read ages ago in her S.H.I.E.L.D file about her training and their indication of the secrets that Natasha kept.
Natasha Romanoff had grown up hidden, a secret in her self. She was living proof that secrets could kill.
If it had been practically anyone else, Tony would have ignored them and continued on his own path, ignoring the interruption. But since it was her...little as he liked to listen to someone else, in this case he knew he had to.
Because he knew that what she said was true. Some secrets aren't meant to be revealed.
That is, until they must be.
When Tony met the Barton family, he immediately knew what secret that Clint and Natasha had worked so hard to protect. And he realized why it was so desperately vital that particular secret remain one from the world at large.
Clint's family was something precious, something outside the crazy world occupied by the Avengers and those who stood with them. Clint had made sure of that, made sure that they would be safe, no matter what. Who knew what he and Laura had gone through and sacrificed to make that happen.
Tony would not be the one to ruin that for them.
After all, he knew that some secrets were meant to be kept that way.