And Away They Did Run:
To be clear: dating a secret assassin-spy is not exactly smooth sailing.
Pepper feels simply helpless sometimes, and it's not a feeling she's used to. Not a feeling dating Tony ever really provoked, because she'll always eventually figure what Tony's up to and he's legitimately scared of her. Pepper is used to being in control, to feeling powerful. It's somewhat of an advantage in her life, to be controlling.
Natasha Romanov cannot be controlled, and she is not scared of Pepper.
She is, however, scared of vulnerability. They work on that-slowly learning more about each other, Pepper learning about how difficult it is for Natasha to be open about herself, learning to appreciate what Natasha has already shared with her. Pepper understands, she really does. She understands that Natasha can't tell her about her missions, understands that sometimes Natasha will stand her up for a date not because she wants to but because something desperate has come up with work. Pepper's been there, knows that dinner out ranks low on the priority scale when compared to national security, she gets it. This is the kind of lack of control she is learning to handle.
Then Natasha comes home from a mission one night (and she can't tell Pepper where she was). She's covered in blood, crying softly, bruises beginning to form on her surprisingly delicate face.
It takes serious force to bruise Natasha. Even more to make her cry. And right then Pepper hates SHEILD, for putting them both in this position. Wordlessly, she wipes the blood of f Natasha's skin, hauls her to the bathroom and peels off her suit. She uses her hands, more than her eyes, to check her lover for anything in need of stitches, antiseptic-anything she can fix. Because right now she just wants to make Natasha better again, and she doesn't know how. All she can do is hold her in the shower, wash her hair, support her as she crumples. All she can do is carefully kiss where the bruises aren't.
Once they're clean and Pepper has pulled a loose t-shirt over Natasha's head, the kind they sleep in, and made them both some tea, Natasha speaks.
"I love you," she begins, "I know you feel...like there's nothing you can do to make me better. And it's true that I'm broken but...you hold me together, Pep, and you keep the nightmares away." Pepper had almost forgotten about the nightmares that used to plague Natasha so frequently, before they were dating, and looking back she realizes that in the nearly six months they've lived together, she's only woken to nightmares twice.
"What happened to you?" Pepper asks softly, not really expecting a response, but desperate to know. They are sitting on their bed together, and Pepper puts down her tea to slip an arm around Natasha, pull her back to her chest.
"I had to kill...a woman who...grew up beside me, in Red Room."
"Oh, baby, I'm so sorry. I'm so sorry." Pepper takes Natasha's mostly empty teacup and relegates it to the nightstand, drawing Natasha further in to her shoulder. After a moment or so she begins to softly sing, "Mine eyes have seen the glory of the coming of the lord/he is tramping out the vintage where the grapes of wrath are stored..." Natasha looks up at her.
"Really Pep? The Battle Hymn of the Republic?"
"It was my favorite lullaby when I was a kid."
"Sweetie, that's not a lullaby, that's a battle cry."
"Tell that to my mom."
And just like that they're laughing again.
Pepper wonders if anything will ever be as wonderful as dating her secret assassin-spy.