En route there, Sherlock remembers Mycroft mentioning Coventry on the phone and reminisces about the allegations that the British government allowed the Coventry Blitz to happen, so as not to alert the Germans that their military codes had been cracked. There, his suspicions that a similar situation is occurring are confirmed by Mycroft on board the airplane, which has been filled with corpses. The government had decided to fly a 'dummy plane', so as not to alert the saboteurs yet still avoid genuine casualties, which also explains the involvement of US agents. However, as Sherlock has unwittingly helped Irene, and, by extension, Moriarty, crack the code, the scheme is foiled.
Mycroft claims to merely "occupy a minor position in the government". However, according to Sherlock, he occasionally is the British Government, functioning as the control centre or "clearing house" for all government actions and decisions.