The main exhibit area contains two mini-theaters, each showing a continuous program.

East end theater - A history of submarines; 10 minutes.

West end theater - A tour of the Nautilus; 10 minutes. Particularly good for visitors with mobility limitations which prevent them from boarding Nautilus. Followed by "Steel Boats, Iron Men"; 18 minutes. An excellent short film depicting life on board a modern submarine.

On display in the main exhibit area is a full size replica of Bushnell's Turtle. David Bushnell of Old Saybrook, Connecticut designed and built the Turtle to attack British warships during the Revolutionary War. The attacks Turtle made in 1776 were unsuccessful, but did demonstrate the submarine's potential. The Turtle was the first practical submarine and the first submarine to attack an enemy ship.

Suspended from the overhead in the main exhibit area is a 50 foot long, 1/3rd scale, cutaway model of the submarine USS Gato (SS 212). The model shows the interior and exterior of this submarine in exacting detail. The Gato was the primary class of submarine used by the United States during World War II.

Submarine weaponry displays include a 20mm deck gun carried by submarines during World War II for use against small surface ships or to ward off attacks by enemy aircraft; Whitehead (1918), MK14 (1940), MK37 (1946) and MK48 (1971) torpedoes; a MK49 (1946) mine; a SUBROC missile; and a Polaris A-3 ballistic missile.

The Nautilus Room, located on the upper level of the main exhibit area, contains numerous artifacts, photographs and drawings associated with the history of USS Nautilus (SSN 571). The display outlines the history of Nautilus from construction, to its journey under the North Pole, to decommissioning. The Nautilus Room overlooks the scenic Thames River and Historic Ship Nautilus.

Other displays in the main exhibit area are dedicated to pioneers in submarine development; design, construction, and launching of submarines; World War II submarine operations; and submarines and national security.