After you finish Mission 13 but before starting Mission 14, go back to the captain's room and check on his corpse. This will start the Secret Mission.

Simply kill all eight Blades with the Needlegun. Try to keep your distance, and just shoot whenever the opportunity presents itself. You can shoot the claws they fire at you, but it's probably safer to dodge. Use the space to your advantage; this area is gigantic. Try to keep them to one side and swim perpendicular to them, then switch facing quickly with the Bx y/B t, fire off a few shots, switch facing again, and then swim for a few more paces. Keeping the pack of them at a distance is key. Killing the last blade gives you a blue orb fragment.