It had been an accident the first time it happened.
Natasha was arguing loudly, angrily with Clint about something none consequential, and she was so agitated, that Tony reached out to lay his hand on her shoulder in a calming gesture.
But he was used to reaching out to much taller people, Steve for example, and so his hand ended up more on her neck than on her shoulder.
Her reaction was immediate: her shoulders slumped slightly, her face smoothed out and her whole stance got more relaxed. It was only a minute change but Tony noticed it. Clint, in all his yelling, did not.
It only lasted a second, until Natasha realized what had happened and then she briskly brushed off Tony's hand, stepped aside and angled herself away from him.
Natasha hadn't avoided him since she had been undercover in SI and so this stung a bit, but given her reaction to his touch, he could understand what was happening.
The second time it happened was much more of a conscious decision on Tony's part, but he wasn't sure she even realized what was happening.
Natasha had been on edge all day, thanks to their run in with some leftover handlers from the KGB and she was tense and ready to jump at anyone who came close.
Tony still dared to approach her.
"Do you trust me?" he asked her and she scoffed.
"I wouldn't be living here if I didn't."
"Good," Tony nodded. "Then don't bite my hand off okay?"
She was about to question what that was supposed to mean when he cupped her neck in his hand.
The change was instantaneous. She relaxed, almost slumped against him, and then her eyes flew open.
"Wow, I did not know you had a weak spot like that," Tony mumbled against her hair when her head came to rest on his shoulder.
"I didn't either," she said and then pushed him away. "Don't you dare tell anyone," she threatened and then turned around to walk away, leaving a gaping Tony behind.
The third time was deliberately on Natasha's part.
Tony was relaxing on the couch, mindlessly watching TV and just enjoying the feeling of not having to meet a deadline for the next two days when she shuffled in, clad in sweats and an oversized pullover.
She flopped down next to him and then moved around until her head rested in his lap and she was buried underneath a blanket.
"Could you...," she started and then hesitated.
He gently rested his hand on her shoulder and didn't rush her to speak. Tony knew she would when she was ready.
"Could you do the thing?" she finally asked and Tony looked down at her. She had her eyes trained on the TV but he could see that she was nervous.
He was tempted to ask what thing, but he refrained; it wasn't like he didn't know what exactly she was talking about.
"Of course," he said and rested his hand lightly on her neck.
She relaxed against him, practically melting into the couch and they stayed like that for what felt like hours.
At one point she drifted off to sleep, hands tucked between her cheek and his thigh and there was a small smile playing around her mouth.