Indeed, the national flag was the British Union Jack with a swastika in the middle of it. The story is that V, a prior victim of the plague, seeks to usurp the government through a combined effort of eliciting the people's help (which happens at the end of the movie), the assassination of the leader (known as the Chancellor) and the destruction of the Parliament building by using a fertilizer bomb sitting on a train (not unlike the Oklahoma City bombing in the United States, except that that was in a box truck parked in front of the building). So as to correlate all of this to what the art relating to the Guy Fawkes mask means, the depiction of the Guy Fawkes mask, the "V" symbol and the anarchy symbol all at the same time is not-so-veiled threat against the government that the people can and might absolutely rise...
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