This Seeking Tech guide will show you how to beat the last boss in Final Fantasy III Pixel Remaster.
The Cloud of Darkness will mostly use Particle Beam to hurt your entire party. Therefore, you will need at least one character in your party with the Curaja spell so that you can heal a big amount of HP after every turn.
The other party members should focus on using their most powerful attacks and provide backup healing when necessary.
You should also make sure that you are at least level 60. If you are underleveled, then you may not be able to survive the barrage of attacks from Cloud of Darkness.