Nightmares are no stranger to their bed. And although they're something they all share, Pepper knows that for each of them it's something very different.
Tony's are the most violent, the most frightening, and the most frequent—to her knowledge. Some are old horrors, some are new, but it's all the same for him once he's dreaming them. They'd gotten worse after the battle of New York, but then, that's true for all of the, isn't it? But she didn't realize how much worse they'd gotten until after they'd managed to get Phil into their bed and their twosome had become a threesome. On the bad nights, Tony will kick and punch, speaking to something neither of them can see. It takes time to sooth him, but they can usually spare waking him, needing quiet murmurs of reassurance and well-placed touches to scare away the shadows.
On the very bad nights, Tony thrashes and lashes out, yells as he fights unseen entities. Gentle reassurances will do no good here. Phil will restrain him, putting him in a hold that cradles him and keeps him from hurting himself or them, as Pepper talks him down until he wakes, startled and bewildered by their positions. He won't beg them to stay, not out loud, but neither of them would dream of leaving. He'll repeat his apologies, over and over and over, as Phil runs his fingers through the genius's sweat-damp hair and Pepper rubs his back soothingly until he falls asleep. One of them will always remain awake to watch him until the sun rises, keeping the specters of his mind at bay as best they can.
Phil is very different from Tony, in that regard. As with many things in his life, the agent is secretive about his nightmares. They always know he's had one when they find him missing from the bed earlier than he should be without a note to say where he's gone. They know his routine and when he deviates from it, then not all is right with the world. The few times either of them have caught him having a nightmare are by luck. He's completely silent, his body as stiff and straight as a board, his muscles drawn so taught that he shakes. There are times he has woken on his own and times when they've woken him, pale and panting stuck in the fight of his fight or flight instinct. His responses are always terse and clipped, he absolutely will not allow either of them to touch him, and he chooses to leave the room altogether instead. Tony wonders in the beginning if there's something they could be doing to keep him from running from their bed to seclude himself elsewhere.
They learn to read him, over time; Tony gives Pepper a heads up when a mission has gone particularly bad. Cold aggravates his old wound—even if he won't admit it—so on winter days when Pepper catches him grimacing and touching a hand to his chest when he things no one's looking, she knows to prepare for a particularly rough night. The best they can do is just wait him out, until he's had too many sleepless nights, until he's too tired to push them away, until they press him between them and hold tight until his body suddenly grows limp, like he's breaking, and he gives in. Until he breaths shaky breaths against Pepper's collarbone as Tony spends as much time as he can reminding Phil that he's an idiot for keeping things to himself. Somehow that seems to be what helps, because he always looks more like himself the next morning, like he'd misplaced part of himself and had only needed them to help him find it.
Pepper doesn't have nightmares when they're with her. She can't possibly have them when she's lying between them, Tony pressed up against her back with a hand on her hip as she lies with her head pillowed on Phil's shoulder. It's only when their bed is empty, when she's alone, that she has them. When there is no one there to comfort her, when Phil and Tony are out saving the world and there's no way for her to know if they're alright, nightmares come for her. Maybe Tony never made it back from Afghanistan. Maybe Phil never made it back from Puente Antiguo. Maybe Tony didn't make it through that hole in the sky. Maybe Phil never survived his confrontation with Loki. Who knows, maybe those things are real. Freshly woken, she has no way of knowing with neither of them there to tell her otherwise.
But logic wins out, she reminds herself that they've made it through all of those things, and as she dries her tears on her nightshirt and declines JARVIS's gentle offer to phone one or both men, she tells herself they'll make it through this, too. Pepper pulls herself together, because no one's going to do it for her and she's not about to let herself fall apart. They must know she doesn't sleep well when they're away. Or maybe they don't. But either way, neither of them will protest when she throws her arms around their necks and pulls them in close when they return, even from routine missions. More often than not they smell like blood and sweat and dirt, but it's all proof of life to her. Her boys are home and even if they've brought fresh nightmares with them, she's sure they'll make it through.
They always do.