Crisis Core Final Fantasy VII: Reunion has plenty of missable trophies/achievements for you to unlock, especially during the main story. The Master Mako Stone Miner is one such Trophy/Achievement.
Preventing the Materia Room from Being Shut Down¶
In order to even get started on this, you will need to unlock the corresponding missions related to this trophy/achievement. Once you start Chapter 2, you will have to speak with Tseng in order to progress the main story. Ignore this and exit the Briefing Room to have a conversation with Kunsel, who will take you out of the Shinra Building and into Sector 8 of Midgard. As soon as you’re outside, go right back through the alley and inside the Shinra Building again.
(1 of 3) You’ll need to step outside first to Sector 8
Once back inside, head to the back of the second floor and interact with the door with an orangish outline to head to the SOLDIER Floor. After a short conversation here, ignore the Briefing Room and find the save point in the area. Near it will be another door, labeled Materia Room. Go in here and speak to the Researcher with the orange icon to unlock Mission 8-2-1.
Do this mission to unlock another, which will in turn unlock more. In total, there’s six missions to do here, although the later ones will get a bit tough, especially when you reach the 4 stars difficulty ones. Each mission will grant you a Mako Stone as a reward, but you need to do all six of them. One trick that stayed from the PSP version of the game is the ability to skip the normal enemy encounters by hugging the edges of the area. If you’re only going straight to the main enemy in each mission, then this allows you to skip the optional fights along the way.
(1 of 2) Head inside the Materia Room
Head inside the Materia Room (left), where speaking to this Researcher will unlock the first mission of the chain (right)
The final mission in the chain, 8-2-6, is probably the toughest one, as you will face two Deathclaws at the end. They have quite a bit more HP than the other enemies in the previous 4-star mission, but they are weak to fire (both missions have enemies weak to fire). In fact, you can get a 
Fira Materia from one of the chests in the same mission, which can help things along during those final two missions. You can also just run around and try your luck with the DMW, hoping to get good rolls on it.
However you do things, once you complete all six missions and have the six Mako Stones, report back to the Researcher to hand over each stone one-by-one to not only get some Materia, but also the Master Mako Stone Miner trophy/achievement.
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