The campaign, which has the player being sent notes from Admiral Dönitz, spans 21 missions from the start of the war in 1939 to the end of the war in 1945, and includes attacking fleeing Polish navy destroyers during the invasion of Poland, hunting British shipping off the English coast, penetration into Scapa Flow, assisting in the invasion of Norway, Blitzkrieg and Dunkirk evacuation ("Dunkirk little ship" Sundowner appears in this mission), then battling in the North Atlantic, before passing through the Strait of Gibraltar to La Spezia, severing the British lifeline to Malta, Operation Drumbeat, attacking in the Caribbean, attacking Arctic convoys to the Allies ultimately gaining the upper hand in the Mid-Atlantic gap, repelling the D-Day invasion and finally escaping to Buenos Aires, Argentina at the end of the war, whereupon Dönitz sends a final message.

[5][6] Silent Hunter II was developed with multi-player support as a notable feature.

Furthermore, connectivity to the separate game Destroyer Command (also released by Ubisoft) was available, which enabled sub and surface ship combat.

[7] The fan community raised over $7000 for an unofficial patch development project called Projekt Messerwetzer which ultimately fixed the issues.

[11][12] In June 2009, after many years of commercial non-availability, the game was re-released on the digital distributor gog.com.