To help you form your cabinet, the game provides a choice of staff from the three main political parties, with each ministry having a crucial role to play in the rebuilding of your country. But beware: your choices may place you at odds with the Army, whose commanders who have their own agendas and, in some cases, will seek to undermine the reforms you have in place. You can fire them, but that is never the end of it. This forces you to think wisely on your choice of ministers.

Gameplay takes place during seasons, in which you can make decisions, encounter various people, monitor imports and exports, read reports, and arrange loans through the IMF. Every decision has repercussions in the game, each choice affecting your future: either as a President elect at the next election... or deposed by your enemies in the next coup d'etat.

One of the most intriguing and unique aspects of Hidden Agenda is the encounters. You will have encounters with various kinds of people, including the public, teachers, doctors, soldiers, etc., all of whom will present you with dilemmas. You can consult with your cabinet to set new reforms in motion or to ask advice on matters of state, but they will not always tell you what you want to hear. The game does allow you to consider some options, but at times you will be faced with a crisis that requires an immediate decision—and that decision may not be what you wanted, or will negate the plans you have made.

The number of possible scenarios in the game is seemingly endless. For example, in one game I was able to halt the rampage of death squads, while in another, other nations I thought were my allies carried out their own motives and goals surreptitiously. From w