A variety of missions are given over the course of the game. You, the squad operator, choose which missions to take.
Missions fall into a variety of categories. Each will have a main objective. Additionally, a standard plethora of safes to crack and guards to steal from are available to provide a way to earn more credits during a mission.
Here are the different types of missions
Detention Center: These missions will have a large area with one basic guard in the center overlooking the captive. Your goal is to free the target in the detention center. The target may be either a prisoner or one of the agents not currently on your team. Successfully evacuating the prisoner will yield a bonus cash reward, while escaping with a fellow agent will add them to your squad for your future missions.
Nanofab Vestibule: While most if not all maps have a Nanofab Vestibule that can be re-purposed for a small variety of purchases, these sites contain one Nanofab Vestibule designed for combat, giving you a much wider array of Augments, Weapons, Programs, and usable items to choose from.
Executive Terminals: These sites will have a terminal which upon being accessed will release the item "Site Plans" which upon level completion will add additional options of missions to be selected from.
Vaults: Vaults have an area which upon entering are blocked by a laser fence, after which there is a terminal. Upon accessing the terminal you gain access to what are essentially four safes surrounding the terminal. Past the terminal will be a second laser fence, blocking off two pillars which contain a Cultural Artifact, which take up an inventory space and are sold for credits upon completing the mission.