I read it on AO3... The only thing I remember about the story is a scene (possibly the opening scene)... Clint is captured and tortured. Coulson's team comes in and they find a man on the ground that has bled out from a fingernail to the carotid. Clint is found chained naked to a table a little farther into the room.
and that's it. Put those skills to use!
Pepper tries to get Tony to sign off on her quitting her job because she doesn't feel that she can do it but Tony has none of it. Eventually it comes out that Pepper got pregnant by her asshole fiancé (named "James"?) who believes that the baby is Tony's, and believes that Pepper should, effectively, "get back in the kitchen" and quit working. Pepper's kind of shocked and winds up giving back the ring.
"James" isn't really the focus of the story so much as Tony stepping up to the plate and being a damn good and loyal man even while being his erratic, quintessential Stark self: proposing, taking care of Pepper, creating a whole new fabric and designing her wedding dress. (Making Pepper worry that the whole thing is a game and he'd get bored and drop her like old tech, unceremoniously dumping all the wedding planning on her...)
A few more tidbits: Pepper is bound and adamant that she will not be giving birth to "Iron Man's baby" (only for the tabloids to report that exact thing and make her blow her top a little). The baby turns out to have a congenital heart problem (inherited from "James", spurring a moment that goes something like Doctor: "You know the baby isn't yours, right?" Tony: "The hell that baby's not mine.") and Tony shows Pepper a miniature miniature arc reactor for if the baby might need it.
I think the title was something like "New Man of Iron" or something like that. I'm pretty sure that it had the word "New" at least.
I'm hoping that this fic hasn't been deleted, because my Google-fu has failed me utterly this time.
Recs for any other fics where Tony is worried about being another name on the "A+ Parenting" list for screwing up his kids and/or turns out to be a truly kickass dad (or at least tries to be) are also awesome.
These recs do not have to be Tony/Pepper fics by any means.