The fort existed since at least the mid-Second Era. The trackless marshes east of Fort Blueblood were notoriously difficult to navigate. A hidden Dark Brotherhood sanctuary was once located at the ancient Argonian ruins of Xith-Izkul, just across the border into Black Marsh, until it was subjected to Purification and left abandoned.
The fort was seemingly still in use in the Third Era, when it was occupied by the Third Empire. A seer named Manduin was buried in the subterranean halls of Fort Blueblood, with not even a tombstone over his head for all his years of service to the Empire. The fort was subsequently abandoned during the relatively peaceful Third Era and fell into ruin.
Circa 3E 433, a local necromancer named Kalthar became disillusioned with the Mages Guild after Arch-Mage Hannibal Traven's ban on necromancy within the guild. Claiming to be reformed, Kalthar remained a guild member, but began plotting to blackmail the local guild head, Dagail, in order to have her promote him out of Leyawiin and step down from her role. To do this, he stole her seer's stone, causing Dagail to be overwhelmed with debilitating visions. Dagail's father, Manduin, had been buried with his own seer's stone, and the Champion of Cyrodiil entered the ruins of Fort Blueblood to locate his coffin. The fort at that time was occupied by marauders, and the Champion was confronted by Kalthar deep within the ruins after recovering Manduin's amulet. However, the Champion successfully returned the stone to Dagail, restoring her lucidity.