Suggestion:
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1. The BBEG wants to unite a large part of the towns / land / whatever to prepare it to be invaded by anything even worse. He doesn't need to set in motion his tyrant scheme as he will be given the town in reward by whoever he works for.
His current plan is to muster the towns army and send them for annexation of the neighboring towns.
You could take the plot from Star Wars, where the army is assembled to defend from the one who assembles it, using the church of Talona or another organization as the ouside threat that all have to unite do defend against
2. The PCs, being in the process of allying themselves with a priestess of Talona, will be accused by the leaders of the town, who are the unknowing puppets of the BBEG and his knowing, evil agents, of being on the side of evil and of trying to usurp the rulership of the town, and will have to find proof of the opposite. This alone should get the players out of the way in the BBEGs opinion. He will ahve some nasty things waiting for them in the prison though to get rid of them.
3. There is a trail of bribes, threats and political alliances pointing to the agents of the BBEG. From the agents can the 3 assistants of the BBEG, the ones who convey his orders to his agents, be found.
4. Several politicians, including one elderly army commander, some diplomat and an adviser of magic have refused the bribes and have been forced on the sideline of the leadership will help the PCs with clues and explain effects of some of the heavier legislations that the BBEG have gotten in place to get to power. They might become the nucleus of the future rulership of the town.
5. The BBEG himself poses as an incompetent politician amongst the leaders of the opposition of his own puppet government. This lets him discover real opposition threats early and send others to remove them and at the same time is the perfect way to conceal himself as the puppet master.