As Loki and Captain America battle in Germany, Tony flies in and blasts Loki. He lands and points his ion blasters at Loki, who surrenders. On the plane back Tony and Steve watch him just as Thor shows up. They fight but eventually get Loki back to the Helicarrier.
When Loki escapes, Tony comes to the realizations that Loki is the kind of Villain who wants attention. And he'd go somewhere where he's center stage. Tony stops and realizes that Loki would got to Stark Tower, and the remaining Avengers head there.
Tony arrives at the tower first and see's Loki in his penthouse. He gets out of the Iron Man suit, and makes his way inside. Loki asks if he's going to appeal to his humanity, but Tony plans to threaten him. He offers Loki a drink as he makes his way to the bar. Loki tells him that he has nothing to fear, given that his army is coming. Tony says that he should fear the Avengers: Earth's Mightiest Heroes. He lists off all the members and tells him he's made them all angry. That was part of Loki's plan, and Tony tell him it's not a good one, since they'll come for him. Even if they can't protect earth, they will avenge it. Loki makes his way over to Tony and says that the Avengers will be too busy fighting him and places the tip of his spear on Tony's chest. It does nothing. He attempts to mind control him again, but it doesn't work. Tony quips about performance issues and Loki throws him across the room. Then out of the window. He calls down one of his suits in time and flies back up. He tells Loki he didn't just piss off the Avengers, but also Coulson and blasts him before going to fight the chitari coming through the portal.
After the chitari are defeated, the Avengers corned a beaten Loki at the tower. He awakens and see's them all, and decides he'll take Tony up on that drink. Tony is seen smirking at his comment.
Most ship them based on their morally grey decisions, although Loki is more like this than Tony. They both also have snarky interactions with each other and other characters.
On AO3, it is the most written ship for Loki and the third most written for Tony. It is the sixth most written in the Marvel Cinematic Universe tag.