Yes it is quite tricky…
However it is not that hard, all you need to do is NOT help them (the other factions) focus on Synedrion only missions, don’t save the others let them burn, instead just search the map and get your stuff like that, you can still trade with them even if you don’t save them and even hire recruits. Also when you get closer to the end it is very easy to make a mistake when you select the research because this will determine you ending. Make sure you only select the faction you want the end for when picking your research and DON’T research the “Alternative” that will screw you up I did this three times before I worked it out, it nearly drove me crazy! Anyway, the key is only select the RESEARCH related to your desired ending, just because the others are there in the queue does not mean you must pick it. There are a total of 4 endings but it is very easy to mess it up when your close… Good luck, hope it helped?