The last of the ship's compartments is the Stern Compartment. This compartment is divided into five sections which are: After Escape Trunk; After Machinery Space; After Crew's Berthing; a storeroom; and the Stern Room. The After Machinery Space contains the ship's atmosphere control machinery, the air conditioning, and various controls for the ship's hydraulic systems. The After Crew's Berthing is made up of bunking facilities for the crew, a washroom and laundry room, a Nucleonics Laboratory and a Sick Bay. The Stern Room storeroom is the largest repair parts storeroom onboard.

In the Stern Room we find the last stop for propulsion shafts before they pass through the pressure hull and attach to the propellors. The large hydraulic rams for the stern planes and rudder are located in the after end of the compartment. They pass through the pressure hull at this point and operate the planes which enable the ship to dive and surface.