Cryptic will keep on developing the stuff they like the way they like it.

Act 1: It was a dark, stormy night when a major conference was held. The conference went bad but you managed to save the day.

Act 2: Some big and powerful (Necrons and their pawns, Bug monsters, Space Zombies, Liberal temporal hippies, the Nonsense Empire, Sela the Undying etc), come up with something to destroy everything you hold dear.

Act 3: When all seems lost someone detroubles the fucupulater in order to repickle the babble. You have to help him to pick some packatan pocks from the Puck system.

Act 4: It was all a rouse, the current big bad managed to attack the UIP (Utterly Important Planet). You arrive alongside a massive fleet and watch a lightshow and fireworks for 20 mins while the devs throw everything and the kitchen sink in your generic direction.

Act 5: The big bad was, in reality a nice guy and it was all silly misunderstanding. You make peace and everything is cool. Unfortunately, renegade elements (Icon Necron the Half handed, Ketracel intolerant bugs, the Zombie Queen, The Strong Minded Weaks, Dinos with freakin lasers on their backs) of the big bad refuse to make peace. This way the STFs don’t feel so out of place.

Go through all the official missions and you will see the pattern.

From here: https://forum.arcgames.com/startrekonline/discussion/comment/13487425/#Comment_13487425