Black Seas is a side-story to Fallout: Equestria, set more then a decade after the epilogue. It follows the adventures of a pirate named Captain, a silver-tongued zebra who is left for dead after his crew mutinies against him and tosses him out into the irradiated ocean. Fortunately, he lands on one of the many still-irradiated beaches and survives; though his body pays the price as it struggles to continue with all the radiation that has seeped . Eventually recovering thanks to the help of the Followers of the Apocalypse, Captain sets out determined to get a new ship and revenge on his old crew. However, he might learn that there may be more to life then looting and exploring the world along the way. Emphasis on might.
Captain is a veteran pirate, and a notorious one at that, having sailed the seas for over twenty-five years and causing trouble wherever he went. Unfortunately, even the mighty fall, as he discovers one day when he wakes up in a hospital bed being treated for advanced radiation poisoning after having been dumped into the ocean by his own crew. After recovering, he is determined to find a new ship and seek revenge for the mutiny. However, his goal seems to get more complicated as the New California Republic as well as various other fractions in Equestria are determined to prevent him from causing more trouble and bringing chaos back to the land.
- Captain: A zebra pirate that goes by no other name, he is infamous for his silver tongue and trickery. His roguish ways are frowned upon by those living in Equestria and his companions, but turn out to be necessary even the post-SAR country.
- Lightning Bolt: A black pegasus who has a knack for technology, he proudly claims that his Stable was one of the most successful as they lasted a few years after the Day of Sunshine and Rainbows occurred; only opening their door after the NCR insisted that it was safe for them to leave the Stable. However, his odd habits and even stranger vocabulary makes Captain wary of the ecology-loving stallion.
- Terramorpher: Often called Terra for short, she joined Captain and Lightning Bolt after a situation involving them and a group of Traffickers, Her mood is often akin to that of an upset manticore, but has been relatively friend in a few situations.