A major focus of the museum is the fate of the clandestine immigrant ship the Af Al Pi Chen, which means in Hebrew “nevertheless” or “despite everything.” This name symbolized defiance — Jews would come to their homeland “despite everything” — despite British opposition and their blockades. This is demonstrated by short movies, and the boat itself is available for viewing in the front courtyard.

After the rise of Nazi Germany, and especially after the Holocaust, many Jewish survivors desperately sought to reach Palestine. However, the British White Paper of 1939 severely limited Jewish immigration to Palestine during and after WWII. The Jewish underground, as well as the Haganah (which was the precursor to the Israel Defense Forces), organized illegal immigration through sea routes.

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The Af Al Pi Chen was originally a U.S. Navy vessel used in World War II (a tank landing ship or LST) and it was purchased and refitted by Mossad LeAliyah Bet, the organization responsible for the overall organization of illegal Jewish immigration. The Af Al Pi Chen set sail in 1947 carrying hundreds of Holocaust survivors and Jewish refugees from Europe. To avoid being detected by the British, the passengers were confined to the hold of the ship in extremely crowded conditions. Nevertheless, the ship was detected and intercepted by the British and the passengers were sent to internment camps in Cyprus, as was routine for intercepted immigrants at that time. Hence, Holocaust survivors who had been rescued from concentration camps now found themselves in yet another concentration camp run by the British. There was a slight silver lining to this in that the camps functioned almost as extra-territorial territory of the Jewish nation, and the immigrants were prepared for their future life in Israel, including learning Hebrew. After the establishment of Israel in 1948, those interned in Cyprus could enter the new state. The ship was incorporated into the Israeli Navy.

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A number of movies can be seen about illegal immigration, including "From Shore to Shore," a 17-minute immersive show aboard the Af Al Pi Chen illustrating the refugee experience, and "The Struggle," a 15-minute film detailing the efforts to bypass British immigration restrictions. The movies are in Hebrew but English subtitles can be requested.

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There are descriptions of different campaigns by the Israeli navy within the museum building.

There are also many varied exhibits on the grounds of the museum. These include INS Mivtach, Israel's first missile boat. It was launched in 1967 and participated in significant naval operations, including the 1973 Yom Kippur War. The vessel is open for exploration, and offers insights into its combat systems and crew areas. INS Gal is a German-designed submarine that was commissioned in 1975, and which served in various Israeli naval missions before being decommissioned. Visitors can tour its interior to understand submarine operations. The museum also displays the bridge of the INS Dakar submarine, which tragically sank in 1968. An emergency buoy and personal artifacts from the crew are also shown.