To earn an S Rank on a mission, you need to earn at least 130,000 points when scored at the end and you cannot have used any items that restrict you from getting such a rank. These include items like stealth camouflage, the chicken hat, and other items, which all tell you that you'll be restricted when you look at their descriptions. Most of your score will be made of the time bonus, which means that you'll want to focus on speed more than usual. Cutscenes do count towards your time, so skip them when replaying Main Ops.
The methods below assume that you've already beaten every Main Ops at least once before and have gone through the entire story, so if you're going at some of these S Ranks earlier than that, you may have to think of other things to use if something mentioned here isn't available to you just yet. It's also assumed that you're skipping all cutscenes when going for S Ranks so as to avoid repetition in instruction. D-Dog, a sneaking suit, C4, and your best Wu S.Pistol are part of the presumed loadout unless stated otherwise.
Main Ops 00: Awakening
Now that you've played through the mission and have seen the cutscenes that set the story of the game, you can skip them all as soon as they appear. You cannot, however, skip the slow crawling at the start of the mission. Just speed through the mission as fast as you can, and you should have no trouble getting an S Rank on it.
Main Ops 01: Phantom Limbs
To get an S Rank as fast as possible, ignore getting the intel and head straight to Da Ghwandai Khar. Tranquilize all soldiers at the outpost and then reach Kaz; taking the outpost over will allow you to call the chopper in to pick you up here instead of past the Skulls, which also completes a mission task. As long as you do all of this quickly, you should get more than enough points for an S Rank.
Main Ops 02: Diamond Dogs
This mission doesn't have a ranking, so you don't have to replay it again.
Main Ops 03: A Hero's Way
The fastest way to complete this mission is to pack a sniper rifle to kill the commander, which you may as well do from further than 100m so you can fulfill a Mission Task. After killing him through a window in his building, run out of the mission area to finish the mission faster than you would if you had to wait for a chopper to pick you up.
Main Ops 04: C2W
Instead of doing anything that you're supposed to, just select the LZ directly above the Eastern Communications Outpost and use the minigun to take out the three pieces of comms equipment. Destroying all of them while still in the helicopter will result in the chopper just flying around for a bit and taking off again with you in it, giving you an incredibly short play time.
Main Ops 05: Over the Fence
If you didn't get an S Rank on your original run of the mission, at least you'll have a better idea of what you're doing this time. Make your first target the crack in the wall just to the left of the barracks itself; it'll have another crack on its left side. Climb up this crack and you'll be able to enter the backside of the building that the engineer is being held hostage in. Once there, hold up any other soldiers inside and get them to lay flat on the ground so they can't pose a threat any longer. Then go for the engineer and pick him up to Fulton him from a safer distance (Fultoning makes noise, of course) or Fulton him through the hole in the roof of this very building. Whichever way you go about it, you'll want to locate a material container while remaining undetected and Fulton it to get yourself out of there.
Main Ops 06: Where Do the Bees Sleep?
For this mission, make your chopper as defensive as possible and use the LZ directly on top of Smasei Fort. If you're lucky, you'll be able to land without any of the soldiers identifying you specifically and will instead focus only on the chopper. Whichever situation plays out, run towards where the Honey Bee is and pick it up, then dash outside to trigger two cutscenes. As soon as you regain control, sprint out of the outpost area until the Skulls leave; this will render all soldiers previously affected by the mist unconscious, which will allow you to safely call another chopper in to Smasei Fort to pick you up without any issues.
Main Ops 07: Red Brass
This is a quick S Rank that you'll earn very easily, especially in the post-game. After arriving in Wialo Village, just wait for all three commanders to show up and Fulton them when they arrive. One of them will drive in with a few of his men; Fulton them as well, since there's a Mission Task related to it. That should be all you have to do to get your desired ranking.
Main Ops 08: Occupation Forces
There's a really easy way to finish this mission that you'll also be using for the Subsistence version of this mission. Use the western LZ and run on the road towards Guard Post 06; when you hear the tanks coming, hide behind a rock near the road and wait for them to pass. Try to jump out in front of the first tank when it gets very close (alternatively, park D-Horse on the road), which will cause all three vehicles to stop moving. Fulton all three out of the area immediately and then call a chopper to pick you up nearby to finish the mission with a new S Rank.
Main Ops 09: Backup, Back Down
Bring D-Horse and some phantom cigars with you and start off at the northern LZ. You'll want to look on the map for an intersection north of the Yakho Oboo Supply Outpost and park D-Horse a bit north of a large rock near the road. This rock should be big enough for you to crouch behind. Wait here a little while and eventually one of the targets will come up the road, stopping to make D-Horse move off the road. When this happens, extract the vehicle and return to the LZ. Use the phantom cigar to make time run out completely, then call a chopper in to leave the area.
For whatever reason, not being spotted and not leaving a trace will automatically give you an S Rank.
Main Ops 10: Angel With Broken Wings
To get an S Rank here, just charge into Lamar Khaate Palace at night and immediately tranquilize as many enemies as you can, and try to Fulton the armored vehicle as well. This should prevent Malak from going anywhere, which means that you don't have to do any more traveling. Put the entire enemy presence at Lamar Khaate Palace to sleep, then call in a chopper to pick Malak up and Fulton out any prisoners that you can reach while you're waiting. When the chopper arrives, pick up Malak and take him into the chopper to finish the mission.
Main Ops 11: Cloaked in Silence
You should have gotten an S Rank when you played through this mission during the story. If not, replay it and only defeat Quiet by marking her and then calling a supply drop in on her head. This will stun her a bit, and doing so twice will result in her passing out. This will also fulfill all four Mission Tasks.
Main Ops 12: Hellbound
One of the most important aspects of finishing the mission quickly is to have both delivery points between the power plant and the central base camp unlocked. You need to reach the delivery point in Serak Power Plant completely undetected. After this, interrogate a soldier to find Emmerich's location, then take Emmerich out of the area to make Sahelanthropus appear. After this, you need to evade Sahelanthropus and get into the chopper without it noticing. A good way to do this would be to leave Emmerich at the closest LZ, then run to the second one so Sahelanthropus follows you to that area. When Metal Gear is far enough away, run back to Emmerich and get into the chopper before he can spot you again. You may very easily score over 200,000 points if you have even a bit of trouble with Sahelanthropus, so you can spend a lot of time in this last part without losing your S Rank potential.
Main Ops 13: Pitch Dark
A suppressed lethal weapon is good to bring, just so you can shoot out lights.
You may find it easier to run along the side of the large rock formation east of Masa Village to avoid everyone there. When you approach the village, focus on Fultoning as many soldiers as you can, leaving the area far enough to trigger a checkpoint to save your extraction progress. Try to clear out the eastern half of the oilfield so you can use the east gate to cause more checkpoints, and put a lot of focus into shooting out as many lights that you think might be a problem for you. Lights remain broken after a checkpoint reload, so doing this early is extremely useful.
When you're satisfied with your takeover of the south end, try to reach the oily separator tank and place some C4 on it. Then head to the control room and shut off the pumps, but don't blow the C4 just yet. Return to the west entrance and stand on top of a resource container before blowing the tank, then use the container to extract yourself back to the ACC.
Main Ops 14: Lingua Franca
Use the LZ that's the most north of the ones available. Instead of bothering with anything else in this mission, look at the mission area on your map and you should see an inward angle between two edges on the northern perimeter. Head there, and as you do so, you'll find the Viscount being protected by a single soldier. Take care of the soldier and extract the Viscount, then leave the mission area. You'll be able to call in a chopper right on this position if you don't feel like physically leaving the area yourself.
Main Ops 15: Footprints of Phantoms
This S Rank is easy. Just focus on extracting everyone in the area that gets in your way, and then make sure you Fulton both prisoners and the Walker Gears at the village for more points. Once they're all gone, leave the mission area however you feel is easiest for your situation and you'll be done. Remember that you can run out to a checkpoint to make the game save your progress on removing soldiers.
Main Ops 16: Traitors' Caravan
The easiest way to finish the mission is to run straight to Nova Braga Airport, then head to the northwest area and approach the truck, which will be parked and unmanned. Just run straight up to it to trigger the Skulls to attack. After they show up, Fulton the truck as soon as possible and then run to a material container in the area, which you'll use to return to the ACC.
Main Ops 17: Rescue the Intel Agents
Land at the western LZ and run straight to the intel team member who's being hunted down. You should be able to get to him in the forest without any issues, but you may have to tranquilize a few soldiers so you remain unseen. Rescuing him will give you the location of the second intel team member, who needs to be extracted by chopper. Getting to him is nothing special, but you may find a fully armored soldier in the area. You should try to use the LZ east of here as a safe place to finish the mission.
Main Ops 18: Blood Runs Deep
First, go to the Bampeve Plantation and find the first of the six targets here. Extract him and use the delivery point here to travel to the mine in a flash. From there, enter the mine's mouth and locate the children. Assuming you're doing this after you've beaten the story as suggested, you'll be able to extract all of them for an easy completion. The injured child will not move, so you can extract him right away. The other four will wait by the locked gate up ahead; tranquilize them and Fulton them, then return to the delivery point to move out of the mission area/use a resource container to return to the ACC.
Main Ops 19: On the Trail
A reliable way to get an S Rank is to use the eastern LZ and run straight to the mouth of the crevice leading to the Ngumba Industrial Zone. You'll be able to find The Major there before his subordinate arrives; just extract him and run out of the tiny hotzone to finish the mission.
Main Ops 20: Voices
The key to finishing this fast is the stun arm, but D-Horse would help minimize travel time. If you're having a lot of trouble charging the stun arm, then bring the water pistol/have it dropped down to you before you enter the testing facility.
Since you want to finish the mission as fast as possible, get to the central building of the industrial zone as fast as possible. There may be a minimum of five soldiers that you should preferably tranquilize in order to get to the testing area without being spotted, so getting there is only a matter of time taken and isn't going to pose any difficulty. Just dash into the building, trigger the cutscene, and start fighting the Man on Fire. When you're engaging him, try your hardest to fully charge the stun arm and let it loose to defeat him. If you didn't cause the tunnel to collapse by getting too close to it, then you should be able to run out of the tunnel when the Man on Fire is defeated to finish the mission.
Main Ops 21: The War Economy
The fastest way to earn an S Rank is to not worry about any of the Mission Tasks whatsoever, unless you can manage to Fulton out both the commander and the arms dealer. Instead of entering through the main gate protected by a watchtower and a security camera, pick the lock on a gate south down the same wall and run along the southern wall until you can make it to the airstrip. Just make sure that you keep an eye on where nearby enemies are so you can get there without being caught. Additionally, any lights you shoot out will remain broken if you do have to restart from a checkpoint, so keep that in mind as well.
When you get to the airstrip in the middle of the area, crawl or crouch-walk even more to the south than you were before so that the snipers atop the main building won't be able to spot you as well. You may encounter a Walker Gear on the way to the west side of the airport; hold him up from behind if you can and extract both the soldier and the machine. Try to slip onto the roof of the main building to find the commander, but wait until the arms dealer joins him so you can extract him for more points. If you can wait long enough, the two of them will walk outside with their skin exposed, providing you a perfect time to tranquilize and extract them.
There are some material containers that you can use to extract yourself out of the area in the southwest corner of the airport. This will help in finishing the mission faster.
Main Ops 22: Retake the Platform
There is no ranking for this mission, so there's no need to replay it.
Main Ops 23: The White Mamba
This S Rank should only be attempted after you've upgraded the Fulton Device to properly extract children. A highly-upgraded stun arm is going to be really important for lowering your mission time here. Just Fulton all of the child soldiers to force Eli to be completely alone, or use a fully charged stun arm blast to instantly KO anyone within 50m of your position (as long as Eli is within range). Make sure you can put him in the chopper without any hitches, and you'll have a quick and painless S Rank.
Main Ops 24: Close Contact
Start the mission using the northern LZ, since that's closer to Guard Post 20. Just head to the guard post, find and extract the prisoners, and then leave the hotzone. There should be a material container around the guard post that you can use.
Main Ops 25: Aim True, Ye Vengeful
Use the LZ at the north end of the map and run down to the guard post. Since there aren't many child soldiers here anyway, you'll easily be able to find the leader and Fulton him (or all of them) out of the area. The prisoner is too injured to be Fultoned, so call a chopper to the southern LZ and run down that way, Fultoning the escaped prisoner as well. It's a really quick mission, so you'll be done with everything in a few minutes.
Main Ops 26: Hunting Down
Use the southern LZ, and arrive there at night (of course). The trafficker and his men are easy to track; they start off from Guard Post 14 and move upwards into the predicted field of movement on the iDroid's map. All six of the total men will be moving very cautiously through the area. If you can, try to tranquilize them all without being spotted and extract them all to fulfill the related Mission Task. If you intercepted the group before they got too far from Guard Post 14, then you shouldn't have a long distance between you and leaving the mission area, so you may want to consider just running out of the area instead of waiting for a chopper.
Main Ops 27: Root Cause
This mission is easy enough that you can get the Mission Tasks done at the same time if you play your cards right. If you arrive at night, you can tranquilize some of the soldiers on the way up the hill and reach the prisoner before he gets into the truck. Tranquilize him or just get close to him if he starts walking over to it, then put him in the passenger seat and drive away yourself. Going north up the road with the target is a quick way out.
Main Ops 28: Code Talker
Bring D-Horse for this mission. You'll want to ride straight up the shallow river, past the Skull cutscene, up until you can slip right underneath the ledge they're sitting on. Keep riding to the end of the cliffside and hug the left side of the area until you're out of reach and can get to the mansion. Doing this while being completely undetected may take a couple of tries, but you can live with being caught here. Scale the cliffs left of the mansion and get to the back door. Toss a magazine or shoot a suppressed weapon to distract the soldiers outside the back door and then either tranquilize them or sneak past them into the mansion. Once inside, sprint down the stairs all the way to Code Talker and skip his cutscenes.
You'll have to do the slow walk up the stairs as Code Talker provides story information. Once you can run again, call your chopper to land on the LZ to the north and sprint to it to finish the mission. You should be able to get by the Skulls on the way to the chopper just fine, just make sure the puppet soldiers don't overwhelm you and Code Talker.
Main Ops 29: Metallic Archaea
When you return to this mission, you should do so as you follow the same instructions for Main Ops 42, which is the extreme version of this same mission. Bring the Hail MGR-4 at *7 and have Quiet use her Sinful Butterfly to provide cover. The two of you will work together on one specific member of the Skulls until they're neutralized; Fulton them away and work on that Mission Task as you blaze through the enemy forces much faster than you did before.
Main Ops 30: Skull Face
For this S Rank, instead of slipping through enemy lines to get to Skull Face, you'll want to instead sprint nearly the entire way there while being as hidden as possible. Before the first gate, try to stick to the right and fire a shot near the sniper to distract him, giving you the space to continue past the gate. Getting to this gate unnoticed is important, as it will give you a checkpoint if you can do so. For the next area, try to stick to the right, but also try to distract the sniper here as well. If this fails, dash for the next area and try to stay alive. You can stick to the left side all the way to the final hangar, which holds the staircase leading up to Skull Face. When you get to him, skip everything to finish the mission as soon as you can.
Main Ops 31: Sahelanthropus
You should have no issue earning an S Rank here unless you have to retry dozens of times without restarting the mission entirely. To make things easier, come back with stronger equipment like the Hail MGR-4 *7 and the Battle Dress; you can see the specific suggested weapons in the story page of Chapter 2.
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