Basically, the group could choose one of two things...1) Have the world die a slow death by erosion...or 2) Save the world, but release the power of alchemy upon the world starting wars, strife, etc...They chose 2 to stop the destruction of the world...I believe the next game will pick up where some of these wars are starting...
So after the Mars star was dropped into the tower, the power of alchemy was released...The towers were destroyed, and Jenna's parents and Isaac's dad revive...They go back to Vale, to find out it was destroyed, though everyone from the village is safe...Alex, who had been pursuing the power released by alchemy, was held back by some force (to an eternal punishment, I assume)...
Perhaps in the next game, Alex finds some way to release his "curse"...