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).