Equestria has been destroyed by a Flood of giant proportions. Though they had time to prepare, many ponies died out, unable or unwilling to believe it. The existing order is gone. Princesses Luna and Celestia have disappeared completely, and the divided lands are loosely ruled by the Monarchy of Queen Cadance and King Shining Armor. However, many Islands have rejected this rule and deign to rule only themselves.

The ponies of the world now live on the patches of land that were not drowned by the waters. Dozens of Islands dot what used to be Equestria, and the open sea is now the great highway for civilization. The ponies have adapted, as they always have.

Things have changed more than that. The animals are no longer always peaceful. Weather rules itself, and Magic is severely weakened. Nopony can figure out why. Instead of bringing back the old order, they have moved on. Ponykind now leads a stable life on the seas, complicated only by the occasional storm and group of pirates.

The bearers of the Elements of Harmony have their own ship, making their own way in this brave new world. Their lives have finally stabilized and they are content.

But nothing of the like ever lasts, and dark clouds loom on the horizon for the 14 sailors on The Free Mare.

Set after the ending of Season 2.