The following are all the achievements that will unlock as you progress through the Story of Metal Gear Solid V: The Phantom Pain. There are a grand total of 50 story missions.

Awakening
Complete "PROLOGUE: AWAKENING" mission.
This is the very first mission in the game.

Phantom Limb
Complete "PHANTOM LIMB" mission.
This is the second Story mission. It follows the prologue after a few cutscenes and introduces you to the open-world nature of MGS V.

Beekeeper
Complete "WHERE DO THE BEES SLEEP?" mission.
This is mission six. In MGS V you don't always have to do the missions in the exact order they are numbered. Many times several of them are available at the same time.

Gears Turn
Complete "HELLBOUND" mission.
Mission 12.

Caravan (Secret Achievement)
Complete "TRAITOR'S CARAVAN" mission
Mission 16.

Voices (Secret Achievement)
Complete "VOICES" mission.
Mission 20.

Immortal (Secret Achievement)
Complete "METALLIC ARCHAEA" mission.
Mission 29.

Skull (Secret Achievement)
Complete "SAHELANTHROPUS" mission
Mission 31.

Disappearance (Secret Achievement)
Complete "A QUIET EXIT" mission.
Mission 45.

Truth (Secret Achievement)
Complete "TRUTH: THE MAN WHO SOLD THE WORLD" mission.
Misison 46.

Accomplished
Complete all mission.
Assuming you did all missions in numerical order, you will earn this after finishing mission 50.

These achievements are tied to the Story missions but aren't earned by simply beating the missions.

Apprentice
Complete a mission using a Combat Unit staff member.
Once you progress far enough in the game to unlock the Combat Unit group for your Mother Base staff (Around Mission 8 or 9) you have the option to select them to use during missions instead of Big Boss. During your Sortie Prep, go to Select Character and choose someone other than Big Boss. Please note that a Side Op does not count. It must be a full Story mission. Mission 9 is the easiest to do for this achievement.

Executed
Complete all mission tasks.
Each of the story missions has objectives that must be completed. Some of them are required to finish the mission, others are secondary tasks. The tasks will be unknown till you complete the mission, afterwards you can see what tasks remain non-accomplished on your mission select screen. I recommend finding an in-depth guide that lists all the tasks if you do not wish to replay every mission.
http://steamproxy.net/sharedfiles/filedetails/?id=528517952

Elite
Complete all missions with an S rank.
S rank is the highest rank you can be scored on a mission. Simply be good at the game and get an S on all 50 Story missions. Generally speaking, to get an S rank you should complete each mission with no kills, never being seen and completing as many tasks as you can as fast as possible.
Browse through Powerpyx's playlist for any missions you need help with:
https://www.youtube.com/playlist?list=PLRr5L69yg_kGiYcnu_StjmzsH7Mnd0fmv

Hero (Secret Achievement)
Obtain the codename "Hero."
To unlock the Hero codename you must get to a total of 150,000 Heroism Points. HP will be earned as you play through the game doing missions, side ops, and building/disposing nukes.

Side Ops are short secondary missions that you can complete for new Mother Base staff members, money and resources. Many of them are to extract someone or destroy a target. There are a crazy 157 side ops.

Undertaken
Complete a SIDE OP.
Do you first side op. The first one should be offered after mission 2 or 3.

Cleared
Complete all "Mine Clearing" SIDE OPS.
Some of the side ops offered required you to remove various types/amount of explosives from an area. D-Dog can help you locate the explosives by marking them on your map. There are only 11 of these side ops.

To the Rescue
Extract a female prisoner.
Most of the people you wil extract will be male. However there are a few side ops where the person you need to extract is female. I unlocked this achievement from Side Op 28: Prisoner Extraction 02.

Achieved
Complete all Side OPS.
There are a 157 side ops, get busy.

Mother Base is your command center stationed on a modified oil platform. You will spent a decent amout of time here and it is the hub for all upgrades and personnel.

Platoon
Increase Mother Base staff to 50 or more personnel.
After mission two you will go to Mother Base and recieve a tutorial on how the Mother Base system works. You start with a handful of men and can increase your staff in two ways. One is to fulton extract soldiers you incapacitate on the battlefield. The other is from randomly generated "volunteers" that you get after doing missions and returning to Mother Base.

Battalion
Increase Mother Base staff to 250 or more personnel.
Same as above but 5 times as many. Just keep Fulton-ing soldiers and doing mission and you will get it eventually.

Army
Raise all Teams/Units to level 50.
Keep improving all your teams as you play through the game. Try and fulton soldiers with B or higher skills to make it easier. Once you've assembled the very best and have all teams at 50 you will unlock this achivement.

Deployment
Complete all key Dispatch Missions.
Dispatch missions are jobs you send your Mother Base staff out to complete while you do other stuff (Unlocked at the same time as the Combat Unit, around mission 8 or 9). Simply have your men complete all the key missions as they are offered and you're set.

Enhancement
Develop 50 or more development items.
After mission two you will go to Mother Base and recieve a tutorial on how the Mother Base system works. There is a great deal of weapons, items and equipment in MGS V. You will have to spend resources and have the proper skill level on you teams to unlock gear. Simply unlock 50 items and you will earn this achievement.

Reinforcement
Develop 100 or more development items.
Same as above but twice as much. Keep building your Mother Base and gathering items.

Locked and Loaded
Develope 300 or more development items.
Yep, keep crafting till you get to 300.

Prosperity
Earn a total of 10,000,000 GMP or more.
GMP is your money, simply keep doing missions, side ops, and find diamonds to earn this over the course of the game. Please note you do not have to stockpile this much money, in fact you can't, as the max amount you can have is only 5,000,000. Spend as much money with out worry.

Architect
Construct all available platforms for Mother Base.
After you complete a few missions, you will be informed that you can increase the size of Mother Base. This takes a great deal of money and resources to do but will increase the items you can develop, the total number of staff you can have and many other benefits. There are 4 levels for each platform. Finish every upgrade and you're done with this achivement.

Big Boss isn't alone in his fight, there are a few companions that can assist you in the battlefield. The following achievements concern them.

Cry Havoc
Make D-Dog available for deployment.
D-Dog can be found early on in the game wandering close to the start of mission 4. Simply stun him and extract him. Once you complete all the mission up to mission 10 return to Mother Base and he should be available to be called out into the field.

Speechless
Make Quiet available for deployment.
You will have to fight Quiet during mission 11. Once you defeat her, do not kill her. Continue playing until after mission 14 then do Side Op 111: Visit Quiet. The next time you go out on a mission, Quiet should be available.

Trusty Steed (Secret Achievement)
Raise bond with D-Horse to the maximum.
The bond you have with your companions increases the more you utilize them during missions. Simply keep riding D-Horse everywhere and you will eventually max out your bond. Oh, and do not shoot him in the head, he really doesn't like it.

Man's Best Friend (Secret Achievement)
Raise bond with D-Dog to the maximum.
Same with D-Horse, call in D-Dog fairly often and don't let him die. D-Dog can be used as a scout to mark everything.

War Buddy (Secret Achievement)
Raise bond with Quiet to the maximum.
To raise the bond with Quiet, try and use a non-lethal weapon in your fight with her. Visit her cell on Mother Base, call her into battle where she can scout an area or provide sniper cover. Also, in typical Japanese fashion, if you stare at Quiet's "bits" for a few seconds you get a few points of bond.

All of these achievements can be earned at any time while in the field, whether on mission or not.

Captured
Capture an outpost or guard post.
Enemy posts are scattered throughout the map. Any place you come across that contains enemy soldiers qualifies as one or the other. Simply eliminate all enemies in the area and this achievement will pop. Much easier to do with guard posts since they usually have from 2 to 5 soldiers.

Extraction
Fulton extract an enemy soldier.
Once you complete mission 2 and go through the Mother Base tutorial you will have unlocked the fulton extraction system. Go out into the field and find any enemy soldier. Stun them or put them to sleep and go up to them and press the assigned key/button to extract them. When you go to extract a soldier you will be given a percentage change of success. You can not extract soldiers that are under coverings and poor weather can reduce the chance. You'll probably end up doing this hundreds of times.

Interrogation
Interrogate an enemy soldier.
To earn this achievement you must slowly sneak up behind an enemy until the CQC prompt appears. Press and hold the correct button to grab and hold an enemy. While holding the soldier, press the keys/buttons to ask that soldier questions. The soldier will tell you information about colletibles or other soldiers in the area. Each soldier can only be interrogated once. When you have the info either kill or knock out the enemy.

No game is safe from the scourge of collectibles.

Reminiscence (Secret Achievement)
Obtain all memento photos
There are only 11 of these and they are earned by recruiting members of the original Mother Base from the Peace Walker game. Many of them are collected during Side Ops but you'll have to find a more in-depth guide elsewhere.

Collector (Secret Achivement)
Obtain all blueprints and key items.
This one will take you a great deal. Blueprints are earned for completing Story Missions, Side Ops, Dispatch Missions, in random spots on the map. Key items are earned for performing certain actions from simply fulton extracting 1,000 soldiers to beating every mission with an S rank. Find an in-depth guide because this one is a doozy. Try this guide posted by InstableMonster in the comments.
http://gamingbolt.com/metal-gear-solid-5-the-phantom-pain-cheat-codes-specialists-collectibles-and-more

Conservation
Extract all wild animal species.
Scattered throughout the map are wild animals. All you need to do is find all 47 animals and extract them with either the fulton or capture cage. Once again, find an in-depth guide on where the animals are, as some of them are very rare and hard to find.
See this guide by Codename S.P.Y. and Scyppend#
http://steamproxy.net/sharedfiles/filedetails/?id=516561727

Intruder
Play an "Infitration" FOB mission.
Forward Operating Base (FOB) missions are missions you can undertake where you go and attack other player's bases to steal, kill, maim, and destroy. Attempt an Infiltration mission and there you go. All you have to do is start an infiltration mission, you don't have to successfuly complete it. FOBs can be built after completing Mission 22.

Deterrence (Secret Achievement)
Develope a nuclear weapon.
After mission 31 you can build a nuke for 75,000 Fuel, and 50,000 Minor Metal from the resources menu. In addition, you lose 50,000 Heroism Points. The nuke prevents your base from being attacked by other players, unless they have reached the Hero codename.

Disarmament (Secret Achievement)
Dispose of a nuclear weapon.
Once you have successful buit your own Nuke or stole one from another player's FOB. You have the option to get rid of the nuke from the resources menu. Do it and you've wasted all your money and rescources for two achievements.

Be sure to Rate and Favorite. This is the first guide I've ever written and I only decided to do it because I work nights and needed something to keep me up. Let me know how it is and I'll continue to make changes as needed. I'm enjoying MGS V for the most part and I hope everyone else is too. Finally, as a plug because it's my guide and I can. Check out my YouTube channel at https://www.youtube.com/user/MrRoxarion where I am not doing an LP of MGS V.