After the end of Chapter 1, Kaz will put a 1984-esque set of rules over Mother Base for the time being, which is meant to help in finding Cipher spies. An appropriate code to mimic, as the current year is 1984. You should check the Battle Gear hangar on the R&D Platform by going downstairs on the first platform of the set so you can use it in Dispatch Missions.
You can skip the missions that are tougher versions of Chapter 1 missions for later if you so choose.
Main Ops 32: To Know Too Much
A CIA agent in OKB Zero has been removed from the area after Soviets reclaimed the base. He needs to be extracted from Soviet hands before he tells either superpower about the existence of the vocal cord parasites. He's being hunted by four Walker Gear pilots, so get behind them and hold them up to neutralize them quickly. The prisoner will be laying in the sand nearby.
Main Ops 33: [Subsistence] C2W
In Subsistence missions, you'll be replaying old Main Ops where all weapons and items must be procured on site. No buddies, no supply drops of any kind, no reflex mode, and no support attacks. You will also not have any reflex mode available to you, so if you're spotted, you'll have to deal with it instantly.
You'll be replaying C2W, but without any starting equipment, of course. You'll first want to run to Guard Post 24 and stealthily take out the soldiers there so you can take their weapons. Next, reach the communications outpost, but watch out for a pair of soldiers on patrol just outside of that area's boundaries. Stick to the high ledges of the outpost and scope the rest of the place out so you can learn where everyone is. A surefire way to not be spotted while destroying the equipment is to remove every soldier from the outpost, so set up a plan to knock everyone out or slit their throats so they're no longer an issue. If you're going with knocking soldiers out, walk far enough away from the other soldiers (40m is safe) with the soldier on your back so you can Fulton him out unnoticed. Below is a rough plan of what I did.
I snuck around the hills to take out the guy all by himself watching the southern road (watch out for three claymores planted up in the slopes to the west). As I did so, another soldier came to investigate, and I managed to get him by hiding the first soldier behind the sandbags of his station until I could knock out the second one. I then went back down the south road to trigger a checkpoint, making sure I wouldn't have to do that again, and then stand on the cliffs to scope out more soldiers. A soldier might spot me when I did this, so I hid until he came close enough for me to get the drop on him. To deal with a pair of soldiers walking back and forth along the higher path area, I hid in an alcove above the path until they passed; I then took one up to my spot and held him up on the ground so he wouldn't go anywhere, let the other one pass back to the west, and then took care of him. After this point, there were few enough soldiers for me to be comfortable with actually getting into the middle of the outpost and handling the remaining enemies.
To exit the hot zone with ease, just Fulton one of the large material containers at the outpost. I managed an S Rank, even with a handful of checkpoint resets after deaths.
Main Ops 34: [Extreme] Backup, Back Down
In Extreme missions, the enemies are significantly tougher than they usually are.
The easiest way to complete this mission for the first time is to simply extract/eliminate only one armored vehicle and then standing still for the remainder of the mission.
Side Ops 113: Eli's Challenge
After his defeat in Africa as the White Mamba, Eli wants to challenge you back at the R&D Platform. Take whatever strong non-lethal weapons you can develop with you to make things easier. A shotgun made to stun can take him down in five hits or so. You'll get his conch shell as a reward.
Side Ops 143: Extract the AI Pod
Return to the Afghanistan Central Base camp and reclaim Huey's AI pod that remained in his lab. Activating it will cause it to skyrocket back to Mother Base.
Side Ops 144: Secure the Remains of the Man on Fire
The Soviets have recovered the body of the Man on Fire and have brought him to Yakho Oboo Supply Outpost. His body is laying out in the open on the helipad in the yard of the main building. Get close to it to put the man to rest for good.
After a little while, Kaz will give you a tape of Huey being asked questions about the AI pod.
Main Ops 35: Cursed Legacy
Some of Code Talker's research materials are about to be picked up by XOF, which is now back to working under Cipher after the end of Chapter 1. You'll need to be capable of Fultoning the containers out of the area, which you should already have been able to do way early into the story. The most optimal thing you could do is have the Fulton Wormhole upgrade to make things go as smoothly as possible.
Land by the southern infiltration point and interrogate enemies until you learn the locations of the two containers. Then run up to the first one or try to take care of the soldiers guarding it so you can Fulton the first container out of there. For the second container, just stand on top of it as you extract it and continue to hold the same key/button so you can immediately be sent up to the ACC and end the mission instantly.
At this point, the children on Mother Base will have likely made their way out of the Seychelles by sneaking into shipping containers. You'll receive a set of Side Ops with the objective being to bring them back.
Main Ops 36: [Total Stealth] Footprints of Phantoms
Bring D-Dog so he can locate all enemies for you and . Try to slip through them and Fulton out as many as you feel comfortable with extracting, then run out into the field and trigger a checkpoint so you don't have to do all that nonsense over again. Just work on getting everyone out of the area, then Fulton the Walker Gears and call in a chopper to land on-site to pick you up (assuming you've destroyed the anti-air radar). It's really that easy.
Main Ops 37: [Extreme] Traitors' Caravan
Just like before, tranquilize as many people at the guard post you start by and look in a tent for an intel file. You can alternatively try to book it towards Nova Braga Airport and locate the truck here before it takes off (do not extract any materials containers, though). If you get close enough while it's parked, the Skulls will infect all nearby soldiers; ignore that and Fulton the truck, then hop onto a material container and finish the mission with ease.
After a while, you'll eventually get a cutscene upon returning to Mother Base of an interrogation, as Kaz and Ocelot have finally figured out what happened to the third missing English vocal cord parasite. After this, you'll get a key item and will be able to develop a new piece of buddy equipment.
Main Ops 38: Extraordinary
One of Ocelot's informants sent to research the Man on Fire and the other child has been killed, but has placed his report in a film canister at Spugmay Keep. When you arrive, focus on neutralizing and extracting all enemies in the area so they're no longer a threat, then check the picture that Mother Base sends you when they're done decrypting it for the location of the film canister. It'll be in a crack of one of the pillars of an archway shown in the picture. Exfiltrate the area, preferably by chopper, once you get the canister.
Note: There's an important prisoner at Guard Post 24, who is required to develop the fifth level of the Wu S.Pistol. You need to extract him for a mission task anyway, so you may as well grab him as soon as you feel like it.
Main Ops 39: [Total Stealth] Over the Fence
This is a pretty simple mission in terms of objectives. You'll just have to extract a prisoner out of the Wakh Sind Barracks. As with the other Total Stealth missions, it's a very viable strategy to Fulton out as many soldiers as you feel comfortable with, then getting far enough from the barracks to trigger a checkpoint so you don't have to do it again. You may only have to do this once or twice. To save yourself some time after extracting the prisoner, use a nearby material container to Fulton yourself back to base.
Main Ops 40: [Extreme] Cloaked in Silence
If you did the original version of this mission, you'll know exactly what to do to finish this version easily: drop supplies on her head. The only significant change here is that you'll want to make sure that you don't get hit by Quiet until the supplies are just about to drop on her head (<10m). Her shooting you will prevent her from jumping out of the way, therefore inflicting some stun damage on her. You can't get hit, however, because this will kill you. Just pop your head out from behind cover for a split second. Additionally, you should bring the weakest equipment you've got so your supply drops cost far less than they should.
You'll find that a supply drop will inflict much less stun damage to Quiet than before. This just means that you'll be spending more time setting up these drops until she finally falls. If sandstorms start to flurry up, just sit tight and wait for it to end. Once again, the supply drop method should take care of the S Rank and the mission tasks all in one go. When you decide what to do with Quiet, you'll find that she looks like another sniper from a different time. This outfit can be made for her after you finish this mission.
Side Ops 145--149: Search for the Escaped Children
To continue the story, you'll need to eventually bring all five children back to Mother Base. They're spread out in multiple areas, and the only way you can Fulton them (as this is far faster to do than extracting by chopper) is to defeat Eli in Side Ops 113 for the upgrade blueprints. Finding the children isn't hard if you have D-Dog with you. Bring some kind of stun shotgun for the third child to use on some bears cornering him.
If the next mission isn't unlocking, then try listening to all tapes marked with yellow dots, as these are the "essential" ones that are more story-related than most.
Main Ops 41: Proxy War Without End
Bring a good rocket launcher for this mission so you can deal with a chopper.
One side of the civil war going on in Africa has hired you to help them, which involves you taking down some enemy vehicles. If you've upgraded your arm's mobility to the highest possible, you should be able to run up to each one as they drive towards the middle of the mission area. To stop them (and therefore allow them to be Fultoned), you'll want to try laying some C4 down and blowing it up in the general proximity of a vehicle. After Fultoning or destroying all four targets, the final target, a gunship, will appear. Take this last target down and leave the area to end the mission.
Kaz will call to tell you to return to Mother Base as soon as possible. It's about Eli.
Main Ops 42: [Extreme] Metallic Archaea
For this mission, you need to fight the Skulls at Nova Braga Airport once more, except it'll be harder to kill them and easier for them to kill you. Bring Quiet with you so she can provide cover fire, wear the strongest Battle Dress you have (and a bandana if you have one), and pack your two most heavy-hitting primary weapons. A good choice is a highly-upgraded Hail MGR-4 grenade launcher; mine was at *7.
Even with the Battle Dress, you're barely going to be able to withstand any attacks, but if Quiet has the Sinful Butterfly, she can provide ridiculously strong cover fire for you. First, you should wait for Quiet to take a shot at one of the Skulls; one shot from the Sinful Butterfly should completely eradicate their tough shield. After this, batter the Skull with grenades and other weapons until its health drops to a minimum. If Quiet doesn't neutralize the Skull, then you will, and you should be able to extract them when they're defeated. If you can extract them all, do so, and you might finish all of the Mission Tasks AND get the S Rank in one playthrough of this mission.
To unlock Main Ops 43, just complete a few Side Ops. It should only take about three or so missions to get it to unlock.
Main Ops 43: Shining Lights, Even in Death
Men inside the quarantine platform's laboratory have been infected with a new outbreak of vocal cord parasites. The communications from the lab are dead, but this could lead to two scenarios. One: The surviving members, aware of their infection, are refusing to speak. Two: Everyone is dead. It's time to find out how they're doing.
Walk through the quarantine tent and proceed with the tasks given to you.
Main Ops 44: [Total Stealth] Pitch Dark
It's a return trip to Mfinda Oilfield for this mission, but nobody can know that you came here. To avoid having to sneak through Masa Village, run to the east around the large rock formation east of the village and continue from there up towards the oilfield. The smartest way to finish the mission for the sake of finishing it is to completely clear the entire outpost of soldiers so it's just you and the objectives. Once you've gotten everyone out of the base, plant some C4 at the tank, turn off the machinery in the building, then stand by one of the large material containers before blowing the C4. As soon as you do, hop on one of the containers and extract yourself out of the area.
You'll eventually get a sixth tape of Ocelot questioning Huey, and after listening to it, you'll be asked to return to Mother Base after a few more missions. It's time for Huey to be put on trial.
To unlock Main Ops 45, you'll need to listen to all of the more important tapes up to this point, have a maximum bond with Quiet, and not have the butterfly emblem in the logo design for Diamond Dogs. You'll also need to do a few more missions first. The next main mission will make you lose Quiet as a buddy, but she can come back easily afterwards. If you would for whatever reason not want this mission to occur (which you will have to play eventually), then you can put the butterfly emblem somewhere in Diamond Dog's emblem design to prevent it from happening. Since you can get her back, there isn't really anything to lose; if you don't use Quiet as a buddy aside from maxing the bond, then you theoretically have even less to lose.
Side Ops 150: Secure Quiet
After fulfilling the above requirements, you'll be asked to bring Quiet back to base; she's been captured by the Soviets. Bring the Hail MGR-4 grenade launcher, the FB MR R-Launcher, the Uragan-5 pistol if you have it (if not, then just bring the Wu S.Pistol like usual), and the best Battle Dress you have as a uniform. For headgear, put the standard bandana on if you have it. You should be able to get an S Rank your first time through Main Ops 45, so don't put the Infinity Bandana on. It'd also be handy if you have your bionic arm upgraded to the most potential it could possibly have. If you couldn't tell, you'll be pushed immediately into Main Ops 45, and it's going to be a pretty big fight.
Sneak into the building surrounded by the most soldiers when you reach the guard post, where you'll find some intel on Quiet's location.
Main Ops 45: A Quiet Exit
Upon dropping down near Lamar Khaate Palace, Code Talker will tell Big Boss some things you probably already figured out about Quiet. Quiet will free herself once you get close enough. Tanks will approach from the distance to prevent the two of you from leaving quietly. Fight off the rest of the tanks as supplies are dropped down to you automatically; Quiet will mostly serve as recon to identify tanks' locations, but you should tell her to provide cover fire so as to kill any troops on the ground. It's going to be a very long fight against tons of tanks, so get used to things quickly.
Once all of the tanks are taken care of, travel with Quiet to the landing zone in the distance. When you regain control of Big Boss, look for Quiet near a tree on a hill in the area.
To get Quiet back, simply replay Main Ops 11 seven times, with all instances ending with sparing her. It's a pretty odd way to make her come back, but it works.
Main Ops 46: Truth: The Man Who Sold the World
After Huey's trial, you'll likely unlock this mission before Main Ops 45. There's nothing wrong with playing them out of order. You'll be recollecting your memories from the hospital here. Do not skip any cutscenes until you've taken some digoxin to get you back in the game. After that, everything is the same until you escape the hospital, in which you should stop skipping cutscenes again.
After reaching the credits for this mission, do not skip them, because there is some timeline information that would be skipped along with them.
Complete "TRUTH: THE MAN WHO SOLD THE WORLD" mission.
For a bit of clarification on the events told in this mission, click the spoiler below. Spoilers for the first games in the series are involved as well, so if you plan on playing Metal Gear and Metal Gear 2: Solid Snake on either the MSX2 (Japanese-only console) or through the Metal Gear Solid HD Collection (the only official English translations of these games) on the XBox 360, then avoid the spoilers altogether.
After the credits' timeline scroll is the just-as-important title dialogue, where Kaz and Ocelot talk about their futures.
Main Ops 47: [Total Stealth] The War Economy
Just like before, you need to locate a CFA official before you do anything else. D-Dog is highly useful here as always. An arms dealer will arrive in a chopper a few minutes after the mission starts. Try to quickly pass through the eastern half of the airport so you can see the western side on the other side of the airstrips. You should be able to easily get to the west side by going around the southern side of the airstrip.
If you can, try to get to the roof of the main building on the west side and wait for the arms dealer and the official to leave the building. Then tranquilize them and Fulton them away and simply ride a material container out of the mission area.
Main Ops 48: [Extreme] Code Talker
Bring a tranquilizing sniper rifle to fight off the Skull snipers that ambush you in the forest on the way to Lufwa Valley. A single shot from them will very likely kill you, so you're going to want to crawl between large rocks to use as cover as you fire a shot at the Skulls. If you have D-Dog with you, he'll be able to locate the Skulls until they're fully aware of your presence, in which case he'll likely be injured and sent back to Mother Base. This sniper battle, if you choose to go at it like a proper sniper battle, will take a very long time.
When approaching Code Talker, don't worry yourself about Fultoning everyone out of Lufwa Valley before getting to him, as the soldiers will re-station themselves around the mansion when you reach him. As soon as you skip the cutscenes where you first meet him, call the chopper towards the northern LZ. Head out the back door of the mansion and move to the LZ; to get rid of enemies looking for you, shoot them in the legs, where they have no armor. They'll pass out after a few seconds. You can also try to sneak up to the tank so you can extract it as well, but if things go sour, run up to the tank and see if you can extract it before it starts moving.
Main Ops 49: [Subsistence] Occupation Force
For this mission, you'll want to sprint straight towards Guard Post 06 as fast as you can in order to reach the convoy before they go too close to the middle of the mission area. Hide behind something when they get close, then intentionally jump out ahead of the tank in front so it spots you. This will stop the entire convoy, which should allow you to simply Fulton all three vehicles, but you have to do so from their sides so they don't drive into you. A good spot to wait is behind a rock south of a small building on the road. It may take a few attempts if the tanks feel like being able to hit you with their bullets from any position you're in.
Main Ops 50: [Extreme] Sahelanthropus
Like Main Ops 42, you'll be more focused on combat this time around. This fight is against Sahelanthropus, however, so you'll want to bring a Hail MGR-4 grenade launcher and a Falkenberg rocket launcher (FB MR R-Launcher) at *5. If your versions of these weapons are better than the suggested levels, then this is only an advantage to you. You don't really need a tranquilizing pistol, so replace it with whatever you want, as long as it's a damage-inducing weapon. Wear the Battle Dress and the bandana if you have it.
Sahelanthropus will not have any new attacks. Simply fight him again with these far superior weapons, which deal far more damage than before, and you'll defeat Metal Gear in about ten minutes or less. If the other child appears, shoot him with your pistol to disrupt Metal Gear's attacks and get an opening. This will also fulfill a Mission Task.
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