Vashyron, Zephyr, and Leanne's journeys throughout Basel are spread across sixteen chapters. Each chapter follows a general flow of an introductory sequence followed by accepting a request from one of the Cardinals. Players then receive the means to expand their travel across the multiple levels of Basel through new Energy Hexes. Objectives will often lead the hunters to dungeons, where they'll battle a gauntlet of foes before encountering a more powerful boss enemy in the way of their goal. After battling their way out of the dungeons, players can then choose to end the chapter by returning to the home base in Ebel City.
Each chapter also boasts a number of sidequests which players can undertake by accepting requests from the Hunter's Guild in Ebel City. Ending the chapter also cancels any sidequests in progress, so players wanting to finish any should do so before choosing the option to move onto the next chapter from the home base chalkboard. Be forewarned, you receive extra Hunter Points for finishing side quests, which consequently awards with items and gun parts.