Clint is in a relationship with Phil (possibly married to him) or at least *was* until Phil "died". Clint (and possibly Natasha) have entered the secret base where Phil and his AOS team are currently located. At the end of the day, when everyone's headed for bed, Clint follows Phil into Phil's bedroom to share Phil's bed as they used to do. Phil doesn't remember their personal relationship due to memories being lost during his "resurrection". Clint thinks Phil must be an imposter/LMD/whatever, bashes his head against the wall, knocks Phil out and ties him to the bed with his tie in order to secure him for questioning.
I remember there's a Princess Bride reference over a flash drive in a desk drawer (the one containing info on the TAHITI project that May dug up out of Phil's grave).
I hate it when I "lose" stories, so thanks in advance for any help in locating it.
ETA: Unknown Unknowns by eleanor_lavish
Thanks to fiveforsilver for the quick response.