In each mission, the agency infiltrates a facility belonging to one of the corporations. The main objective depends on the type of mission. When playing with the Contingency Plan DLC, regular facilities have a 25% chance of having a random side mission.

In typical missions, the main objective and any other objectives are always optional; it is possible to exit the mission without completing or even attempting them. However, you must always find the exit room and use the teleporter to complete the mission. A mission is failed if all agents in the team are lost in the field.

The mission's type, the corporation, the game difficulty setting and the mission difficulty level determine the number and types of guards and other security measures which will be found in the facility. The available mission options are shown on the world map screen, which shows this information as well as the travel time to reach the mission. Generally, lower mission difficulty levels appear earlier in the campaign, and higher mission difficulty levels appear later.

There are eight types of typical mission:

	Mission	Objective
	Chief Financial Suite	Interrogate the Financial Executive to acquire a Vault Access Card.
	Cybernetics Lab	Use the Augment Grafters to install new augments or augment sockets, and possibly use an Augment Drill to remove a currently-installed augment.
	Detention Center	Rescue a new agent, or an agent lost in the field, or a Prisoner.
	Executive Terminals	Loot the Site List from the Executive Access Terminal to add new mission options to the world map.
	Nanofab Vestibule	Use the unlocked nanofabricator to buy new items, weapons and augments.
	Security Dispatch	Loot a high-value item or weapon from the Secure Locker, and possibly rescue a Courier.
	Server Farm	Access the Primary Server Terminal to buy new programs for Incognita.
	Vault	Loot credits and Research Experiments from the vault.