To get them, you have to find the JTF officer in your area and talk to them. For example in Camp Hudson you find the JTF officer opposite the vendors. In the Base of Operations the JTF officer can be found in the left area of the entrance (south), close to the situation board.
Once talked to the JTF officer, the missions will appear on your map and start by simply showing up at the spot.
For completing missions, you gain XP, credits and also get a blue print for Crafting. Once you have completed all side missions in an area, the JTF officer will contact you and you can get an extra blueprint, usually of higher quality, from them.