Metal Gear Solid 2 plays out like this. Spoilers below but it came out in 2001 so whatever
The bad guy is a former President that knew his job was just as a figurehead, nothing more. He found out the hard way that even his orders came from a cutout.
He recruited "terrorists" to take the sitting President "hostage" so they could "force him" to detonate an EMP over the east coast. The plan is to dismantle the shadow government (actually AI) running the government/censoring public opinion and hopefully free the country
You play as the wide eyed idealistic special forces infiltrator, trained heavily through VR and sent to "rescue" the sitting President from the "terrorist leader" and learn that everything you know is wrong and you were given orders by the AI all along