After launching the game once, head to your config folder of Battlefleet Gothic Armada II, in your appdata folder. You can copy/paste the following in the research tab to access it with this link: %LOCALAPPDATA%\BattlefleetGothic2\Saved\Config\WindowsNoEditor.

Step 1: Find the file game.ini
Step 2: Edit it with a file editor program such as wordpad or notepad.
Step 3: Find the line "bHasPlayedPrologue=False"
Step 4: Change it to "bHasPlayedPrologue=True"
Step 5: Save the file.
Step 6: Restart the game.