The Phantom Pain is a very open-ended game in how you play it, as each mission can be done in many different ways. This guide will attempt to focus on the stealth perspective in missions, with a general walkthrough for each mission, as no single mission will be the same for everyone.
Every mission in the game will have their mission tasks listed (with a number), with them either being designed as mandatory or option. Those tasks marked as optional will be listed at the end of the general walkthrough, but some tasks will be covered in the walkthrough, so if they are not shown at the end, then look there. Also, some tasks are pretty much a no-brainer, such as extracting a target alive versus killing him, so they will most likely not be covered.