Hello,
I'm experiencing a strange case with the shinari's campaign in Normal (playing with Mac OS 10.12.2
When I get the message "destroy he pirate base", the planet doesn't show up on the screen so I auto lose this quest… Out of 20 tries I had this 16/20. Is it something I don't know about this mission or a glitch?
thks

Pretty sure it is, it happen to me on the solarian campaign as well on a few playthroughs, did not managed to find a solution, you can try to look for it with your fleet scanners and upgrading your radar, if the pirate spawns a fleet you can try to follow the direction they came from until you find their base.

I take it when you say it doesn't show you mean the planet is not visible in your starmap despite saying the planet name is like "Magellan 6" on the message you receive?