There were "orders" for each possible problem that could arise. 65 I think it was, was the order given if the Supreme Chancellor betrayed the republic. So even though it was always his intention to use the command, he was smart to embed it in amongst all the other possible commands.
The question is, why didn't the Jedi use it first? Arrogant that they could take him alone?
Well is order 65 G cannon or C cannon.