As already mentioned, the missions in The Phantom Pain are separated into two main types: Main Missions and Side Ops. Main Missions are focused on the story in the game, while Side Ops usually have smaller objectives you can do, functioning as side missions. While most are relatively simple and have no tie-in to the main story, there are important Side Ops that require you to play them in order to advance/unlock Main Missions.
Every Main Mission in the game has objectives you can fulfill, some required to finish the mission (mandatory), with the others being entirely optional. Some of these optional objectives cannot be completed on your first playthrough, either due to time constraints or not having the right equipment needed to do something. It’s a good idea to concentrate on the mandatory objectives first and leave the optional ones for another playthrough.
Something you will notice is that you get graded at the end of each of the Main Missions, with E being the worst and S being the best. There are a number of factors that contribute to the score, and your goal is to get 130,000 points, which is the threshold for an S Rank. There are three Main Missions where you don’t get a rank at the end, which are Missions 2, 22 and 43. Side Ops are not graded at all.
One of the biggest point factors will come from how fast you can finish a mission. Each mission will have some hidden thresholds for how many points you receive from the time bonus, but the general concensus is that the faster you finish a mission, the more points you are going to get, resulting in a higher chance of an S Rank.
Another big chunk of points will come from how you play the mission, whether you use stealth or not. While it’s possible to achieve an S Rank by going commando on the enemies, you will get a little leeway by using stealth. This means not killing anyone, not being seen by the enemy and also doing the mission without having to restart from a checkpoint. It is possible to get around 40,000 to 50,000 extra points if you do everything correctly.