It happens more or less like this:
Tony is in his workshop, fiddling with the biggest waste of vibranium ever made (and, seriously, vibranium? like, what, they discovered it and thought it would be good for making sex toys out of or something?). He hears Pepper coming in, but he doesn't really bother to look up or anything.
He's got a picture of her standing on his desk, these days, in the frame the picture of him and his dad used to be in. Happy thoughts, and all that.
When she gets close enough to touch (he doesn't, but he could. He wants to), Tony figures that it's either coffee or lunch - or on second thought, make that dinner.
"Thank you, yes, there's an empty spot over there if you want to - " and there isn't, in fact, an empty spot where he's pointing yet, but if anyone's going to be shoving papers and models and tools aside, it's going to be Tony, because let's not risk accidentally setting off any bombs again, shall we?
He doesn't actually smell any food, so it must be just coffee. He doesn't smell any coffee, either, but, well, he does smell workshop smells - metal and solder and oil, so there.
"Would you mind - just a little bit to the left," Pepper says, close enough now to smell her, and Tony's seriously reconsidering that whole gentlemanly thing he's got going on here; sure, she'll be busy, with paperwork waiting for her back at the home office, but he's sort of busy, too, so, really, if he's willing to make a few sacrifices, she should be fine with it, too. Surely. "And turn around."
"There's something on my face? Someone upstairs to see me? Is it Rhodey? Because if it is, I'm pretty sure he's not going to mind if I've got a little - " He feels her reaching for his wrist, of course he feels her reaching for his wrist (her hands are still small and soft and strong) but he doesn't really think ... because this is Pepper, and the kinkiest thing they've ever done that was her idea was have him sign paperwork naked which, on reflection, not really kinky. "Why, Miss Potts. Did you just handcuff me to my desk?"
"Yes, Mister Stark. I believe I did." She's dimpling at him. Tony loves it when she does that.
"This is new." The handcuffs look like solid workmanship. He wonders if she got them at a sex shop - on-line, maybe, delivered with discretion, which usually means they wrap the package in the kind of plain brown paper that might as well have 'look at me, I'm a (discretely packaged) sex toy' stamped on it. Not that Tony's got any first-hand experience with those sort of packages or anything. "I like it."
More dimpling. "They were a gift."
Tony's not wearing the suit, so it's really ridiculous to feel like some sort of 'alert: danger!' sign has just started flashing, just outside his field of vision. "A gift." His, then - nobody else is sending Pepper gifts that he knows about - and he would know about it. He's sort of pathetic that way. "It wasn't your birthday again, was it?"
"No, Tony, it wasn't my birthday." Underneath her jacket, she's wearing ... not a whole lot.
It's kind of distracting, making it hard to think, which is unfair, really, because strip-teasing in progress or not, Tony's pretty sure he's not going to get any tonight unless he figures out what the handcuffs were supposed to be a gift for.
"Was there an anniversary? You know I'm really bad at anniversaries."
"You really are," Pepper agrees. "Keep guessing."
Possibly, at this point, it might be more productive to figure out how to pick the lock. It's a mechanical one, so it must be possible. "Okay, all right, so it's not a birthday and it's not an anniversary. What else is there?" Pepper takes off her skirt. Tony's brains do this thing where, basically, they don't do anything anymore. Not helping, clearly. "Can I give up now? Is that a ... thing I can do? Just say: you win, I'm an idiot, I don't deserve you? And then, I don't know, still get sex?"
Pepper smiles. No dimples, but there's a whole lot of Pepper visible by now, so Tony doesn't mind. "Maybe."
She means it, Tony knows. When Pepper says 'maybe', it's not like with other women, who say 'maybe' when they really mean 'yes' (or 'no', sometimes, which is why Tony always made sure he got a 'yes' before he invited people over to the house).
On the other hand, she's also getting quite up, close and personal, so his chances are looking pretty good. "I have absolutely no idea why I gave you a very nice pair of handcuffs, but I'm sure it was for a very special occasion which I'm obviously deeply, deeply sorry to have forgotten about."
"Uh-huh." Pepper starts working on his shirt, which is nice - Tony is all in favor of Pepper taking his shirt off whenever she wants to. "I don't think - that's the thing about handcuffs, see?" He's still showing a fair bit of chest. He's been told it's a nice view. By mostly sober people, even.
His pants are next. Those come off just fine - no problem with the handcuffs there.
"Pep? A hint, maybe?" Pepper is ruthless, yes, but Tony likes to think she's still got a soft spot for him.
He's not sure what sort of hint, if any, is supposed to be conveyed by shoving him back against the desk and kissing him like she's actually trying to blow his mind (bit of a waste of effort, really; it doesn't take that much to reduce what remains of Tony's higher brain functions to mush; just feeling her naked against him is enough to accomplish that much already) but at that point, he figures it really doesn't matter.
"Gift from Natasha," Pepper says, looking smug and a little bit messy and like the only woman Tony will never have had sex with often enough. (Conveniently, he's her boyfriend.)
"From Natasha. And you're sure they're not poisoned or something? You've checked to make sure the key works?"
Pepper gives him this look that makes it clear that she's not a guy. Which, yeah, Tony'd sort of noticed, thanks, but even so. "Tony. It's fine. I've got the key right here, see?" It fits, too. "She's a good friend, really."
"Agree to disagree?" The handcuffs were sort of a good gift, admittedly.
Tony makes a mental note to ask JARVIS to replace them as quickly as possible with an identical looking pair. With any luck, Pepper will never find out.