After winning the twin cities of Ebonreach and Bellhall as a power base, Isaac investigated the occupied mayor's office of Ebonreach where he and his retainers encountered a walking fish-man (or a naga of myth, I suppose), the mysterious Icthyus that had coordinated the Ormican occupation of the city. In the ensuing fight, Isaac's beloved bodyguard Faye was slain, the victim of Icthyus' poisonous fangs.
After holding Faye's funeral, Isaac added finding out more about Icthyus and his people to his campaign goals, believing them to be the cause behind the sinking of Estralis. In dire need of additional forces, Isaac pursued Ned's recommendation of tracking down his brother's bandits, so that they may be recruited to the cause. Within Ted's fortress, Ned beat his brother in a hand-to-hand brawl and killed him afterwards, assuming control of the bandits under Isaac's banner. Isaac then promised to grant Ned reign over the region, naming him Duke Edward of Vaike.
Their next move was to remove the Arcymis forces from an important fort on the border of the nation. With the help of a young woman named Vesper, they found a prisoner by the name of Nah. Nah was a manakete (a direct descendant of divine dragons, with the power to shapeshift into a dragon) and the 'Voice of Naga'; the world's link to the vague words of the Dragon Goddess, Naga (much like the Listeners of the Dark Brotherhood).
Nah lent her divine insight to the Estean campaign after the Arcymians were forced out of Esteos, and informed Isaac of the existence of a divine blade; Curtana, the 'Blade of Mercy', which was held by the ruler of Indartis, High Judge Magister Weiss. A former relic of Isaac's royal family and a work of the manaketes of old, Curtana would allow Nah to directly commune with Naga herself.
Pressing on the Indartis forces was next on the line; on the way Isaac's company encountered and recruited a former Judge of Indartis named Cedric, who had defected shortly after the campaign began. His daughters Eve and Eden accompanied him, and with their help the Esteans successfully infiltrated a village held by the Indartians, freeing the indentured villagers within.
On their way back to the Twin Cities, Isaac's company was caught and confronted by Judge Magister Weiss himself, who freely gave up Curtana to Isaac out of indifference attacking, prompting the grand Battle of the Maelstrom.
Though heavy casualties were sustained (particularly Duncan the monk), the Esteans found themselves to be the victors after slaying two of Weiss' high-ranking officers and fellow judges, prompting a full Indartian retreat. All that remained were the Ormicans in the west.
Before this, Isaac gathered his closest retainers and went with Nah to speak with Naga through the power of Curtana. In a revealing conversation, Isaac discovered that both he and his strategist, Kasumi. were descended from the ancient chieftan Romulus and a manakete woman, making Isaac and Kasumi direct descendants of the Dragon Goddess herself; possessing blessed blood, they were considered to be 'Touched by Naga'. Additionally, Naga elaborated on King Romulus' conflict with the race of fish-men to which Icthyus belonged; the 'Abyssnians', who served their serpentine God-king the 'Leviathan'. The Leviathan had been defeated twice before, and each time it returned to slumber, the Abyssnians had gone with it. The sinking of Estralis and the re-emergence of the Abyssnians meant that someone was trying to summon the Leviathan once more in order to destroy the entire world; using the massive death toll from the sinking of Estralis as a catalyst for the summoning ritual.
After the commune with Naga, Isaac and the others returned to the Twin Cities for a rest. During their downtime in which they recuperated and resupplied, Isaac's vassal named Ririka was put in charge of putting on the first annual Dragon Festival, which entailed several festivities; including a joust, a grand melee, the knighting of the newly founded Knights of the Prismatic Flame, and the marriage of Daud to Kasumi. Isaac's uncle, King Ghayle, and his daughter Princess Kimata, visited for the festival as well, and stayed in the Twin Cities for a time.
Once the festivities concluded and the army was ready to march once more, they moved on to attack the city of Whitemere, where the Ormicans had their strongest fortifications. Shortly before the battle, Daud was attacked and bitten by an Abyssnian, suffering the poison and falling close to death. Nah intervened by stabbing Daud in the chest with Curtana, draining the divine power from the blade and healing Daud with the power of Naga. With the blade drained, the healing was no longer an option in the case of a bite.
The siege of Whitemere was a resounding success and the Esteans pushed back the final occupants of Esteos, as well as taking the general of the Ormican forces as a prisoner. From there they made a direct visit to the Chancellor of Ormica, demanding answers on her involvement with the Abyssnians. She scoffed at Isaac and had her guards attack him and his party, but they managed to escape the city without answers. Ned stayed behind to assassinate the Chancellor before accompanying the others out back to the Twin Cities.
When they returned, they were shocked to find King Ghayle murdered, and Princess Kimata missing. The princess' involvement in the crisis was now suspect, and with all the nations pushed out of Esteos, Isaac's company were free to enter the Maelstrom with the help of Naga, in order to pursue the Leviathan's summoner and the Leviathan itself.
The party fought through the sunken ruins of Estralis and managed to reach the sunken castle. Within they found Kimata, presiding over a black portal in the floor of the Throne room. Varos, a swordmaster who had originally been lent to Isaac by King Ghayle, accompanied the Princess as her bodyguard. She explained that she had developed a disgust with humanity after her beloved mother passed away, a victim of a peasant plague she caught when trying to appease rioters years past. Using forbidden knowledge and magics, she orchestrated the sinking of Estralis with the similarly demented Chancellor of Ormica, killing hundreds of thousands of people and beginning the resurrection of the Leviathan.
The Leviathan's portal used the souls of the dead as fuel, thus preventing those souls from passing on to the afterlife. However, the portal could not be dispelled, except through the summoning of the Leviathan. After battling and defeating Kimata, the disgraced princess explained that the Leviathan needed a divinely touched soul as a vessel, else the portal would remain and trap lost souls for centuries or even millennia to come. This left the Esteans with two options for the vessel; Isaac or Kasumi, who were blessed with divine blood, while Nah remained aboveground keeping the path back to the surface stable.
Isaac and Kasumi both readily volunteered their lives as sacrifice for the Leviathan's return, that they may kill it once it appeared in order to spare the souls of the dead. However, Daud had a realization; when he was healed of his toxic bite by the touch of Curtana, he became 'Touched by Naga' in a different sense; whatever the case, he held divine essence in his body, and he sacrificed himself so that his liege or his newly pregnant wife wouldn't have to. Through Daud's body, the Leviathan emerged from the portal, and after a vicious battle that claimed several lives, Isaac and his remaining vassals managed to slay the Leviathan, sealing it away once more. With the souls of the dead now free to pass on and the threat to the world contained, Isaac and his friends returned to the surface.
From there, Isaac was free to reign over his newly rebuilt country, this time as King Isaac. He, however, had bigger plans...