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Natasha developed a closer relationship with Tony.
He and Pepper have officially broken up and the genius billionaire as Iron Man worked more with the Avengers. Following the falling out of the team due to the Accords though, breaking them into two groups, Tony and Natasha's friendship has further evolved from platonic to more-than-friends-but-less-than-lovers.
They did not talk about it. There was no flirting that happened, no I-love-you's exchanged... no sex. Their actions toward each other stemmed from their emotional attachment, greater than the physical needs. They understood the other even without words. They looked out for each other. They either supported or challenged each other's decisions until they came up with the best plan of action. They felt safer to show their weakness to the other, trusting that they would not be judged nor taken advantage.
When Rhodes underwent a major surgery after their encounter with the rogue Avengers, him and Tony were visited by Pepper as soon as the Stark Industries CEO got back from vacation. It was the first time they saw each other after their break-up almost six months ago. And Natasha could not help thinking that the reunion meant the two were getting back together... again.
So before she got brushed aside by Tony or, worse, before she witnessed them picking up from where they left off and progressing further, she started avoiding the engineer. Natasha cut non-work interactions and literally stayed away from where he was. Whenever Tony was in the compound, she went to attend businesses outside. Whenever he left, it was when she stayed in her room or picked up personal stuff to bring in case she needed to sleep elsewhere.
Like how they never discussed about their relationship that escalated through time, neither did he ask about the sudden drifting apart. Natasha figured it - what she thought about as something more meant nothing to the guy. She was just a ready relief from his stress. A diversion. Probably, even a rebound. Pepper and him were perfect together... why would he consider replacing the good woman with a broken soul like her?
*****
Tony, with his bright mind, could not decipher what just happened. One day, Natasha was enveloped in his arms; three days later, she barely stood within his reach. Her warm aura was back to being cold. Her beautiful face, stoic again. She never talked to him if not for Accords or Avengers-related concerns. He attempted to corner her and ask what was going on between them, but she has gone while he was with Rhodes' physician.
Could it be that he just read it wrong the whole time? That she was just a deeply caring teammate and did not intend to be anything more to him? Or probably, she just got carried away too with the need to belong and be loved.
No, his mind would counter. If everything between them was delusion, then delusional he was.
Did he want her more than just as a colleague? He could not admit... All he knew was her staying away and shutting him out of her life was more painful than his and Pepper's mutual decision to go back to being friends. His chest tightened whenever he thought about the redhead spy. Less than half a year of them sticking around each other, sharing ideas, sharing their nightmares, sharing the good times and the bad, sharing kisses...
He missed her terribly. He needed them to be back to how they used to be.