He is credited with ending the Mỹ Lai Massacre of the South Vietnamese village known as Sơn Mỹ on March 16, 1968, alongside Glenn Andreotta and Lawrence Colburn.
Thompson: What's going on here, Lieutenant?
Calley: This is my business.
Thompson: What is this? Who are these people?
Calley: Just following orders.
Thompson: Orders? Whose orders?
Calley: Just following...
Thompson: But, these are human beings, unarmed civilians, sir.
Calley: Look Thompson, this is my show. I'm in charge here. It ain't your concern.
Thompson: Yeah, great job.
Calley: You better get back in that chopper and mind your own business.
Thompson: You ain't heard the last of this!
While Warrant Officer Thompson did follow Lieutenant Calley’s order to “get back in that chopper”, he did not “mind [his] own business.” Instead he rescued civilians and interposed himself between US soldiers and their potential victims. At one point ordering his door gunners to be ready to fire on any US personnel who continued massacring civilians.
Thompson flew to the Task Force Barker headquarters (Landing Zone Dottie), and angrily reported the massacre to his superiors. His report quickly reached Lieutenant Colonel Frank Barker, the operation's overall commander. Barker immediately radioed ground forces to cease the "killings".
The US chain of command attempted to cover up the massacre, so charges could, of course, not be laid as a court martial would reveal everything. Instead Thompson was awarded the DFC on a fabricated basis (rather than the actual basis which was clearly deserved).
Eventually, news of the massacre leaked and Thompson testified before Congress and in the court martial of Calley that followed. He was vilified by many Americans and received death threats and had dead animals left at his front door. Whether this was because the thought he was lying or because they thought US soldiers raping and murdering civilians is OK I can’t say - probably a little of both.
Of the 26 men charged over the war crime, only Calley was convicted and served 3.5 years of a 20 year sentence.
Thompson remained in the army as a flight instructor for several more years eventually retiring as a Major. He continued to fly in civilian life and participated in several documentary films about the massacre, including the award winning Four Hours in My Lai.