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. Missions may also have secondary objectives that can be completed for even more credits.
While any Corporation can have any type of mission, the Corporation's individual flavor can make the difficulty of missions vary wildly based on your team composition. Pick carefully!
This facility holds the locations of future targets of value. Each mission type provides key benefits to your agents, and while new locations will be presented to you over time, a successful infiltration here will speed up the process and give you more targets of your choosing. The first mission in the game will always be an Executive Terminals mission.
These missions contain one Executive Access Terminal, which, once hacked, can be looted to obtain a "Site List" item. In addition to this, later Executive Terminals missions will allow you to pick one mission of your choosing that is guaranteed to appear, from a list of four.
As soon as the Terminal is looted, guard patrols will change.
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.
Detention Centers may also feature Power Relays: a set of two switches that when activated in the same turn unlock a room with a power console. Activating this console will sell up to 15 of your PWR, in chunks of 3, in exchange for significant amounts of Credits.
While most if not all maps have a Nanofabricator that can be used to make a small variety of purchases, these sites contain an advanced Nanofabricator. The advanced Nanofabricators are capable of making many more items than the smaller ones, and contain more items at once. They sit in distinctive rooms, usually in the center.
Once you exit the Advanced Nanofabricator's purchase screen for the first time, a number of Mainframe devices will restart--this can include the Advanced Nanofabricator. Using the Nanofabricator again will not trigger this effect a second time.
These missions should be undertaken with large credit reserves, as the high-end gear in the Advanced Nanofabricator is not cheap.
Like Nanofabs, many maps will feature a Secondary Server Terminal that can sell you two programs for Incognita. To get the most powerful programs, you have to seek out the black market software engineer ShopKat, who can be contacted only from powerful corporate servers located in Server Farms.
The Primary Server Terminal is located in a large room that will always feature two consoles, which can help locate it. It may or may not have a guard in it, but will also feature plenty of cover. Unlocking the PST lets you buy from ShopKat, who has a much larger and more potent selection than usual.
Once you exit the PST's purchase screen for the first time, a number of Daemons will infest various mainframe devices at random. That damn cat!
Server Farms may feature Techs--civilian scientists who have laboratories on the level only accessible by Dongles they carry on their person. Stealing this by any means will allow you to access their labs, and a free--and usually potent--Incognita program within.
The high-powered elite who run the world's mega-Corporations have access to many facilities that no regular employee can access. They also have an unfortunate tendency to work late nights, well after most of their security details have gone home to bed. Unfortunate for them, but not for you.
Executive Suite missions task you with locating a large office which contains a Financial Executive civilian, and likely at least one guard. If the Executive spots you, he will attempt to flee the level via the nearest Enemy Teleporter.
Your job is to knock out the Executive and have at least one Agent stick close to him so that Incognita can ransack his brain for his access codes. This will take six turns, and halfway through the Executive will summon an Enforcer to come to his defense who must be handled. Don't worry about keeping him unconscious--Executives can't take a punch and will be knocked out for at least six turns no matter what they're hit with.
Your reward is a Vault Access Card, which can be used in at least two of the mission types below--as well as the very large amount of cash the Executive carries on his person.
A Vault is a Corporate storage facility, containing money and objects that the Corporations do not trust to the banking system. The shape and layout of these vaults can vary, but they always contain two features: a terminal room and a case room.
One of these rooms will be normally accessible, and will contain at least one guard or drone. The other will be only accessible from the first, and ONLY if you have a Vault Access Card, which you must acquire from Executive Suites or, rarely, from Monst3r.
The Terminal Room contains a terminal which must be hacked. When activated, this terminal will unlock four Safe Deposit Boxes nearby, which can be looted for large amounts of Credits.
The Case Room contains two locked cases that can be hacked or EMPed open. Each contains a Research Experiment, worth 500 credits upon exiting the level.
Whether you hack a case or the terminal first, the first one hacked will summon an Enforcer to the Vault to catch the security breach. It may be possible to avoid this if you EMP the cases and use a Buster Chip to crack the Terminal, but this has not been reproduced yet and may be a bug.