I personally really like the terrormorph quests, but otherwise I haven’t seen much of the game yet. So if you have any proposals, I’d be really happy to hear them!
Definitely Crimson Fleet. During my first playthough, I still hadn’t done a lot of the main quest, so I felt I HAD to side with the UC at the end just because trying to do Constellation missions while not having proper access to UC space. And I legitimately felt torn and sad for the Crimson Fleet. It was one of the only decently written quest lines that made me feel that.
Spoiler-free answer.
My favourite quest was the treasure hunt you do with the space pirate (whichever side you pick), in particular the last mission “eye of the storm”.
My second favourite is “entangled”, but it’s more because of the “wow” factor at the start. The rest of the quest was standard.
Most of the other quests are forgettable and badly written.
The worst quest for me is “operation starseed”, which feels like a bad Star Trek episode.
Definitely Terrormorph, though the Freestar Ranger quest is nice too. Haven’t gotten around to Shattered Space yet.
Personally I’ve enjoyed exploring outposts and taking out space pirates and spacers.
Though (small spoiler) if you choose to side with the space pirates, you’ll encounter less of these populated outposts to take on because they’ll be friendlies except for the spacers, which really made it less fun for me to explore.
crime doesnt pay. i had this issue too. then my wife sarah morgan yelled at me for siding with the pirates 🙄


