Tony has just returned from a dangerous mission, he's been gone for days and he's sore and in pain but- his wounds are superficial. It's nothing Pepper can't handle in house. It's the first time Pepper is taking care of Tony in their "stable-ish" relationship and Tony is unsure of what to expect when he returns home.
Instead of the awkward tension and restraint that usually accompanied physical contact between them, Pepper is openly loving and gentle with him. Instead of teasing her to ease the tension, Tony can now savor every healing touch in silence. There are fewer boundaries between them. Her touch lingers longer than before. Her face is closer to his. He can stare at her openly. And he can feel her breath on his skin. Each pad of her finger resonates acceptance when in contact with his skin, and it sends sparks everywhere she touches. It's not sexual, necessarily, it's euphoric. He hardly notices the pain, he's too busy concentrating on her and her touch and the way it makes him feel sweet relief everywhere, even inside his chest.
She is letting herself go, savoring his return. She is kissing his wounds, and ruffling his hair. She is letting her gaze stay locked with his a few seconds longer. She is letting her touch and breath wash over his skin and heal him, even the wounds he's buried deep down, the ones invisible to the eye.
When she is finished Tony takes her hand in his and brings it to his lips. He kisses the pads of her fingers and says thank you for taking care of him. He reminds her that she always takes such good care of him. There's a hint of tears in her eyes but she holds them back- he's here now and she need not cry, at least this helps him to the bed before joining him. Tony relives every moment of bliss in his head as he drifts to sleep beside her. Even as he struggles to understand his feelings, he knows he's never felt so loved and he never wants that feeling to go away.
And it doesn't.