Mission Master ...
This achievement is obviously for completing all story missions.
This achievement for most people will pop when obtaining 100% plus completion in Smuggling, Security, Influence and Production and completing the 2 missions for the final boss and the 2 DEA missions.
Note: This achievement is currently known to be buggy/glitchy for no apparent reason.
I had completed all story missions and had 100% plus in all operations, but my achievement tracker was on 99%. At this point in time, no one really can pin point what makes this occur, but there is a solution that worked for me.
What worked for me to pop this achievement was to go into each providence and hit to bring up the option to replay the missions. Now what I did was selected to replay a mission and waited for the mission checkpoint message to pop up on my screen. Once that happened I simply went back into the replay mission option and selected the next one on the list and continued to do so for the rest of the providence before moving onto the next one and repeated the process moving around the map.
For me, my achievement popped using this method in about the 4th providence I tried this method on. Hopefully this method will work people that are stuck on 99% progress on the achievement tracker.
The Peruvian DLC missions do not count toward overall progress on the tracker.
Credit to Karlos Fantano on the ubisoft forums for the solution which helped me unlock my achievement. worked for me
Just worked for me too. A hint is when you get a call from Karen Bowman and you tell her you are heading to the next AO. That means the providence is complete, and you can go to the next one.
The ones that didn't give me a "Mission Checkpoint" noticed I did again
Now on to fixing the The Whole Story, Legendary Hunter, Sniper Rifle, and Sub-Machine-gun Fanatic as they are not unlocking either.
Glad to see people helping others here, as it's the only help we are gong to get it seems.
A update to the post, as I have also had this work for unlocking the "Legendary Hunter Badge and Achievement" here is a screen shot. Just did it a few minutes ago. Going to try this also for the others that are not unlocking too. Hope this helps out with your badges not unlocking. Yeah I'm on a PC too.
Ok just fixed another one "Whole Story: wasn't unlocking either. So when to the last Providence I did in my completed game. Start getting the Kingslayer file and Legends documents after the 4th one I found, the achievement unlocked. 
Last two are Sub Machine Gun and Sniper Rifle Fanatic. Going to continue with this new save and unlock them too. At least Ubisoft knows what is going on now. When you play multiplayer it's not recording all players as picking up the item, file, document, or finishing the mission. So the only way to correct it. Is to start a new save and do the missions, find the items, or documents, or legends yourself.
Like the other posts I've done. here is another achievement unlocked by following the simple fix. Sniper Rifle Fanatic Achievement
Last one to work on is the Sub Machine Gun Fanatic Achievement.
Well that's it guys. I just unlocked the last one that I couldn't under my first save. Even after getting all the weapons. And NOT BUYING anything in the store. This will work for everyone who also has the issues with any Badges or Achievements not unlocking.
UbiSoft PLEASE PIN THIS POST! Or add it to your know fixes, so everyone can stop racking their brains trying to get this Badges and Achievements, You can even remove my name ( I don't care ) Just want to help those with this issue. As it's very frustrating to do everythinng and still not get the reward for it. Thanks
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FIX For Awards and Achievements Not Unlocking Works 100% Pin This Fix UbiSoft
