Merchant and warships of the Equestrian Navy have been destroyed and their crews wiped out by a mysterious creature roaming the depths. Many believe it is a sea monster that has risen from the depths to terrorize ponies sailing the seas. Twilight, however, doesn't believe it and becomes determined to find out what this creature is and put a stop to it before more lives are lost. So the Mane 6 goes on an expedition to find this creature, only to discover that it's not a sea monster, but a submarine, the Ulysses. Twilight and her friends are taken captive by the sub's crew and introduced to their captain who lets them stay in his ship but won't ever allow them to return to Equestria. With no alternative, Twilight and her friends join the crew of the Ulysses and embark on an amazing and life-changing journey under the sea.