So the first arc is the Map and El Dorado. That's obvious. I have an idea for the second arc.
Starting with El Dorado. You go there, there's a boss fight with Kane, then a cutscene where he unleashes something. And that something is a great power known as Obsidian.
Obsidian is the villain for the second arc. He is a mysterious hooded figure whose color scheme is black and purple. He has a legion of Obsidian Colossi (they look like the Colossus from the Wizard spell but with Obsidian's color scheme), and wants to destroy the Spiral.
After the cutscene, there is a boss fight with Obsidian. You can't kill him, so the objective is to survive. When you survive, Obsidian unleashes a cheat that kills you. The screen fades to black, there's the Somewhere in the Spiral thing, and you wake up to see Avery on your ship.
Avery shows a puppet show explaining what happened while you were out and setting up the whole arc. The goal of the arc is to get Obsidian back into his prison.
Obviously, in the final fight, he takes his hood off. KI, you get to design his face.