Tony is a Hydra flunky
There was a very interesting post online that pointed out that A LOT of Tony Stark's actions suggest he was part of Hydra. From weapons supplying to supporting a document that would tie the Avengers' hands to spouting straight-up Hydra beliefs to making his own version of Project Insight, Tony comes across as a perfect Hydra drone. (Even Tony Stark's name on the list of Insight targets could be explained away as misdirection, one Hydra operative protecting another.) What if someone discovered his secret?
***
Tony smiled to himself as he adjusted another angle of his design. This satellite would cement his--and Hydra's--control of the world. The ability to eavesdrop on everyone with a cellphone or computer combined with the fleet of death drones would guarantee Hydra's victory. First the U.S., then the world...
The creak of a door made Tony look up. He froze at the sight of a ghost. Tony asked, "Agent?"
Phil Coulson stepped into the light, his gun leveled on Tony. Phil said, "Don't move, Stark. We've got you covered."
Tony reached to deploy his gauntlet watch, but nothing was on his wrist. Before he could ask how that happened, a woman with long dark hair appeared behind Coulson, twirling Tony's watch on one finger.
Before Tony could order Friday to send a signal to Hydra, another woman came at him. With a few blows she had Tony gasping on the ground, unable to draw breath. The woman kicked him and said, "Hydra scum."
A third, younger woman walked into the room and said, "I've deployed the virus, destroyed the servers, and set the charges. In five minutes there won't be anything left."
Coulson nodded and looked down at Tony. He said, "I didn't want to believe that Iron Man was Hydra. But after we hacked into your systems, it was pretty obvious you were doing everything you could to destroy the Avengers and any other hero who could stop Hydra's plans."
The last thing Tony saw was the stun bolt coming at him. That Coulson's team "forgot" to remove Tony from the building when his house was blown to atoms was just an unfortunate accident.