The decision involving this trophy occurs in Chapter 9 of the story, "The Road". 

This is a part of the second duo of decision-based trophies in the game. Both this trophy and the trophy, Damned if You Do are related to this decision, so if you want to see what the alternative decision would be, refer to that.At the very beginning of the mission, you will soon encounter a freeway sign with two men hanging off of it. You are ordered by Konrad to execute one of these guys, based off what "crime" they committed.
Bucking the chain of command, as the trophy implies, would be attacking the snipers overlooking the hanging convicts, or shooting the rope of one of the convicts. If you go through with this, simply shoot one of the snipers/ropes to start the gunfight. Just one word of advice: take cover behind the ambulance truck to the right before you open fire at any of the snipers. We shot a sniper out in the open, not noticing the ambulance truck. We died very quickly. This isn't the recommended option for your FUBAR playthrough, as this battle can be bypassed by picking the other option.
Once you have made your decision, you will get this trophy when you reach the next checkpoint.