This article is from the Final-Fantasy and other Square Soft Games FAQ, by email@example.com (Nick Zitzmann) with numerous contributions by others.
Basically, there is Benjamin, a boy who was raised by an old man of his
village. One day, while he is with a man on the top of a hill, a great
earthquake starts, and they are attacked by a monster; and it's a very
strange thing, because monsters have never been seen anywhere for a long
time... Benjamin kills the beast, and returns to his town only to start
a journey that will bring him all across the world, until the final
battle with a powerful being called the "Dark King".
There are many differences from this and the other Final Fantasy games;
the world is divided in four parts (and everyone is related to an
Element) linked by a giant Tower, but the tower's doors were sealed
long, long ago, to separate the four regions; in every region there is a
large dungeon (ie the Ice Pyramid, Lava Dome, and Pazuzu's Tower) which
holds a boss monster that controls that land.
Another difference: during the game, some of your actions will modify
the very shape of the world: you start in the Earth region, that is
becoming more and more dry and ill, and you will restore it to
fertility; the Water region is freezing, and you must restore warm to
it, and then open a hole with a powerful bomb in a sealed waterfall that
once used to fill a great lake in Wind's region, and now is sealed; the
Fire region is being shook up by powerful earthquakes (you'll see them
on the world map !) that you will stop, and in the Wind region you will
stop the strong wind that is going to destroy the city. During the whole
game, your party will be composed only by two characters: you and
another, that will often change. The last (and biggest) difference from
other games is there are no battles on the world map, but only in the
locations, and the monsters are visible, and a battle can be started
only by going into them; and, when killed, they will disappear.