Sila, captain of the Sea Shadow, continues her mission to dismantle Red Eye's legacy with her found family crew. The story focuses on their interactions and the lighthearted moments amidst their serious work. The crew includes Nanook (the boisterous helmsman), Tsushin (the quartermaster, chef, and surgeon), Long Yan (the navigator and signalman), Yumi (the boatswain), and the player as first mate. The setting is aboard the Sea Shadow, a prototype submersible vessel, in a dangerous area known as the Dead Zone. Pre-existing relationships between the player and the crew are welcome.