The story is dls's: "If You Had This Time Again" specifically chapter 4!
I've looked through my files, searched tags on AO3, did a bit of Googling and no joy.....
I think the scene I recall was part of a larger storyline. I think Tony might have time travelled back to the battle with the Chitauri in NYC. He talks to Loki during the night hours in Stark Tower's penthouse. Thor goes and rests in a guest room. Tony meanwhile "watches/guards" Loki. Tony removes the gag that Thor put on Loki. They discuss that Loki was not a free agent when he arrived on Earth with the scepter. Eventually, Tony provides Thor with proof of Loki being controlled by another before they depart for Asgard.
I think the story was on AO3 and was written before IW.
Sound familiar to anyone? Any help and/or pointers would be greatly appreciated. TIA.