It references all the stuff out of the original game, pulls it out, and constructs it in the new engine.
'Square actually have a copy of the original Final Fantasy VI inside the Steam release of Final Fantasy VI, and what they do is reference the original copy as a database to pull information such as cutscenes, where sprites are located, how the map is constructed, item stats, AI.
'Final Fantasy VI is sort of unique compared to the other Final Fantasys on Steam,' said modder Christopher Cooper, who goes by the handle Krisan Thyme online. And unlike the typical PC port, Final Fantasy VI contains a surprise secret: a pristine copy of the Game Boy Advance ROM buried in its source code. Final Fantasy VI’s PC port was definitely not built to be fiddled with.