Up until its capture by Shay Cormac in 1752, the Morrigan served as a smugglers’ vessel in the North Atlantic. Following the rescue of Chevalier de la Vérendrye, a French-Canadian Assassin operating in the area, by Shay Cormac and Liam O'Brien from the aforementioned smugglers, the Morrigan was seized by Cormac for use in the Assassin fleet.
The vessel quickly saw action, when it rescued Chevalier's Gerfaut, which had come under attack from several more, smaller vessels.
During Shay’s mission to the Lisbon Temple, the Morrigan remained behind, and eventually passed into the hands of another Assassin following Shay’s supposed death. Months later, she was stationed in New York City, when Shay Cormac and his new allies, the Templars Christopher Gist and George Monro aided him in its re-capture. From this point onward, the Morrigan served Shay’s in his Templar duties, aiding the Templar-supported British Royal Navy in their conflict with the French.
Such duties included capturing French settlements in the River Valley and North Atlantic Ocean, eliminating the Colonial Assassins' presence in the region, and liberating several groups of native Iroquois. In addition to this, the Morrigan traveled the globe to aid Britain's, and by extension the Templars', efforts in the Seven Year' War. These efforts saw her destroying a number of well-known warships.
In 1758 the Morrigan pursued the warship of the pirate-turned-Assassin Adéwalé, the Experto Crede, newly arrived from the Caribbean, and forced it to beach in Vieille Carrière. Two years later, during Shay’s pursuit of Achilles Davenport to the Arctic Temple, she encountered Chevalier’s Gerfaut once more, and this time managed to sink the Man O' War in open combat.
With the ship's armaments and equipment funded by the wealth of the Templar Order, the Morrigan was one of the most advanced warships of her time; she was equipped with state-of-the-art weaponry such as puckle guns, carronades, and burning oil. She also possessed the standard armaments including 34 broadside cannons (with 17 on each side), mortars, and an ice-breaker ram. Despite her smaller amount of cannons on board compare to the Jackdaw (23 cannons on each side), the Morrigan made up for this with the ability to fire twice in quick succession before reloading, allowing her to possess more speed and firepower. Due to the Morrigan's sleek design, she was much faster and more maneuverable than several other ships while still maintaining above average firepower for a ship of her size.
- Shay Cormac - Captain (1752 – unknown)
- Liam O'Brien - First Mate (1752 – 1755)
- Christopher Gist - First Mate (1756 – unknown)
- Argonaut - Sunk during a skirmish.
- Cauldron - Sunk during a skirmish.
- Couronne - Sunk during the Battle of Labrador.
- Equitas - Beached while pursuing Samuel Smith.
- Experto Crede - Beached while pursuing Adéwalé.
- Formidable - Sunk during the Battle of Quiberon Bay.
- Gerfaut - Sunk while pursuing Chevalier de la Vérendrye.
- Pilgrim - Sunk during a skirmish.
- Sceptre - Sunk during a skirmish.
- Storm Fortress - Sunk during a skirmish.
- The Morrigan's default sails and figurehead featured intricate wolves in their design.
- The ship shared her name with a figure from Celtic mythology called "the Morrígan", meaning "Phantom Queen" or "Great Queen" in Irish. She was the goddess of strife, battle and sovereignty. She was mainly depicted as a crow in her animal form, giving the Morrigan an avian namesake along with the Aquila and the Jackdaw.
- The quotes and dialogues of the Morrigan's crew change when Shay reclaims the ship from the Assassins, showing that the crew members that Gist recruited replaced those serving the Assassins. Also, the uniforms and appearances of the crew members change.
- Like the Jackdaw, the Morrigan's equipment at elite level, including puckle guns and mortars, are plated gold but the cannons' appearance does not change. The burning oil barrels become reddish-brown. The Elite hull upgrade gives the Morrigan a crimson colored hull with silver plating on the hull and deck.
- In "A Long Walk and a Short Drop", the flag Shay cuts down from the Morrigan's mast bears the Assassin insignia, even though the flag he flew during his Assassin years did not have such an insignia. It's possible the Assassins switched the flag in the period that Shay was believed dead. Also, despite being a Privateer ship working for the French Navy, it flew the Royal Navy flag in its front mast.
- If the Morrigan was fully upgraded with its default wolf sails and figurehead, her appearance became very similar to pirate hunter brigs that the pirate Edward Kenway faced in his time.
- Historically, carronades were not available aboard naval ships until at least the 1770s.