Level 06: We're Everywhere

South of the 2x shield recharger there is a room that has two hexagonal pillars. There's no way to enter the room from here - but the switches can be shot at. However, this switch won't be active before the mission objectives of this level have been met. Once shot, the switch will activate one of the platforms, as well as opening a secret door back at the beginning of the level, near where the Fusion Pistol is located. By following the secret path that is revealed, you'll enter this room.

Swim into the room and onto the platform in motion. Once the platform crests, jump to the platform opposite - sidestepping will be required. Once on this platform look up. On the walls there are two switches - hit one of these. The platform will rise up and lead to a room stocked with ammo.

On the side of the map near the huge doors that are opened as part of your mission there's an ammo cache alongside one of the outside walls.