Nick Fury had underestimated Phil Coulson once; mostly that was on the Army for having taken Coulson at face value for so long, but Fury should have looked harder anyway.
After a dozen years, Fury thought he knew Coulson well. It turned out he didn't. He knew Coulson's abilities, his skill for both strategy and tactics, his amazing administrative efficiency, his gift at getting agents to rise above their individual limitations. But he didn't really know Coulson.
In 2001, Coulson had argued, successfully, for an increased SHIELD presence in Afghanistan, but independent from and with different aims than those of the US military. So in the run-up to the US invasion of Iraq, Fury expected similar support for a planned SHIELD presence.
After three hours of listening to him reject every idea anyone suggested with a vehemence Fury had rarely seen, Fury demanded to hear what Coulson would suggest instead.
Coulson stood up, took his sidearm out, chambered a round, turned it around and offered it to Fury, calm despite having a dozen guns aimed at him.
"I suggest that if you think I will in any way provide support for this invasion, your best option is to eliminate me as an obstacle now," Coulson said.
Fury accepted the offered weapon and asked, "Are you offering your resignation?"
"Resignation isn't ever on the table for anyone in this room. I'm telling you now that you'll save everyone a lot of time and energy by killing me now rather than having to do it in three months after I've actively worked to undermine SHIELD's plans in every possible way."
Fury sighed. Then he removed the clip, cleared the chamber, and handed the gun back to Coulson. "We're done here, everyone. Dismissed."
Fury called Coulson back into his office the next day; he announced Coulson's promotion that afternoon.