Rather than follow a strict mission structure, Silent Hunter 5 presents players with a large objective then leaves them to rewrite history.

In an overview document, Ubisoft gives the example of supporting Rommel's North African offensive in 1942 by escorting supply ships, hitting the Allies' own supplies, knocking out their fleet, or going directly for the sub and bomber base in Malta.

The campaign features over 160 ports, 70 airbases and 10,500 ships with 250 convoys, supposedly operating dynamically and reacting appropriately to the player's actions.