Alexander Ortega is an outlaw, wanted for the destruction of August, an island in the nightsea. He stumbles into a town called Dry Gulch on the Island of Tombstone, and discovers that the outlaw holding the town hostage, Goldfist, is searching for an island core. After defeating Goldfist, Alex gains access to the core and uses it to gain information that will hopefully lead him back home. He leaves Goldfist in the care of the townspeople so that they may collect the bounty on his head when the Military Police arrive.

Alex arrives on Glory Plateau, and island that has a massive coliseum on its shores where prisoners fight for freedom. After getting captured thanks to the antics of a thief names Erin, he teams up with with Erin and a swordsman named Sayed to fight their way out of the arena. After facing off against an old foe in the ex-Apostle Lucien, the island is taken over by a Black Spot that begins to consume it while Alex, Erin and Sayed make their escape. Alex and Sayed decide to work together afterward and begin their partnership.

After stumbling into Erin a second time, Alex and Sayed decide to work with her to retrieve a logbook that has details on Roald and his journey to a new world. Together they journey to Cragg Hollow, where they find the town is subject to an infestation of mind-controlling masks. After defeating the one responsible for the masks, they gain the logbook and find that it points them in the direction of a 'no man's land' in the nightsea called 'Death's Yard.'

Stealing a Military Police slipship, Alex, Erin and Sayed, find that they have an additional crew member on board in Jean, and together they journey into Death's Yard to find the island of Nowhere. On Nowhere, they face off against the Finger, Mister Deadman, and his Knuckle henchmnen, Bragg and Cragg. After defeating them, Alex and Erin discover an android M.A.R.I. in the ruins who knows the location of Roald's ship. Together, they journey off to find the ship using M.A.R.I. as their guide.

Ortega and his crew arrive on Diamond Peak in search  of Roald's ship. Little did they know that they would meet Runa, an associate of Roald, who had dementia and access to the ship. After gaining access and sending a message that Roald had recorded out across the entirety of the Erth, they run from the Military Police and bounty hunters chasing them, setting their sights on a new island 'Dry Turtle.

Ortega and his crew arrive on Dry Turtle. After setting up the ship for repairs and finding a ride to the Core for Kali, Erin is kidnapped by two slavers called the Harper Brothers. Alex and Sayed rescue her, and along the way, they pick up an itinerant prince named Artur Lopold. During the rescue, the ship is attacked by a Finger named 'Miss Brooke, who nearly breaks it in half. She is defeated by Li Wen and Jean working together. When Alex returns, they promise Artur that they will escort him to Grim Aegis, an island that guards the entrance to the Core.

Alex and his crew are driven to a strange flickering island on the nightsea due to a pirate attack. After stopping for repairs, they explore the nearby jungle and discover a city made of gold. They are attacked by the locals, a people called the Zoan, and their guardian, a former Military Police Commander named James Thompson. After discussing their differences, they go to Zoan's village, where they are attacked by the same pirates, the Benbeck Brigade. Failing to capture the crew, Benbeck escapes with a hostage, calling on Alex to come and fight. Alex and his crew face off with the Benbeck Brigade, revealing the person who hired them in the Finger Miss Glory after their defeat. After Miss Glory is defeated, Alex uses the same island core that built the golden city to recover a ship for the Zoan to escape the island before they succumb to aetheric corruption.