Classified Bay

The Classified Bay was a refitted part of a starship on the ventral side. Classified bays started to be added on after the beginning of the 25th century when stronger and technologically enhanced weapons and other devices started to appear.

Location
As shown on the diagram, on Sovereign Class vessels, the bay would be right in between the ventral phaser array and lower fore torpedo launcher. But on other vessels it would be a little bit behind the main deflector dish.

Contents
The contents, or whats inside of the bays are basically technologically/tactically enhanced weapons, devices or vessels. Stronger alloys and plating were placed around the bay, since most devices in them could/are volatile and mostly prototypes, their destruction/loss could have major consequences, not to the ship but to the designers and Starfleet.