In the middle of the vast sea stand two titans who, in times immemorial, struck each other dead. On the body of one of them, Bionis, biological life has blossomed; in the other, Mechonis, the machines live. They continue the war started by their ancestors: the humans and other races living on Bionis are desperately holding back the onslaught of mechanical hordes.
The game's protagonist is Shulk, a young man living in a settlement on the shins of Bionis. To protect his homeland from the attack of the machines, he picks up the Monado - a sword, whose legendary power can only be coped with by a few. The artifact gives the hero the ability to see into the future and he fights back against the attackers - but he fails to save all of his loved ones. Driven by a thirst for revenge, Shulk sets out to find those who prevent the war from ending.