The royal bodyguard has/have deserted en route. In the sentence, which helping verb, has or have, should be used.
The word bodyguard can indicate an individual or a military unit, and it is not clear how you are using it in your example. If you mean a military unit, then you should put:
The royal bodyguard has deserted en route.
However, since desertion is basically an individual act, it might be better to put:
The royal bodyguards have deserted en route.
It all depends on whether they acted individually or together (under command of their officers).
The noun "bodyguard" is singular. "Has" is the singular verb.
The royal bodyguard has deserted...
This is correct whether the bodyguard is an individual or a collective noun (which is still singular) for a group of bodyguards.
"Have" is correct for a plural:
The royal bodyguards have deserted...