It's not just missions, it's time as well. I'd got all crew loyalty done before the crew got kidnapped, but I went off to do some mineral scanning to research some final upgrades before going through, scanned 2 systems worth of planets etc, and got the 'half the crew liquidated' thing. Not a single mission, just scanning about 8 planets.
Where's the Kaboom? There was supposed to be an Earth-shattering Kaboom!