Hm... If that will not gonna happen then we will not know how did the War begun between the three Factions and how they manage to advance in every technology and researches.
Some of the story is in the lore section of the website and in the instruction manual, as well as the Vanilla/Diplomacy game intro videos.
In summary though, the war began when the Vasari, fleeing from some unknown force that destroyed their Empire, arrived in TEC space. They were initially unprepared but managed to mobilize their industry to start to beat back the invaders. Then the Advent returned, a group of Humans the TEC encountered a millennium ago but banished them for their cultural practices, which were too bizarre for the somewhat xenophobic TEC to tolerate. Naturally, the Advent did not liked being kicked off their home world, and vowed revenge against those that cast them out. Their timing was all too perfect, now as a three way contest, just who would win the war is anyone's game.
The two expansions don't add all that much too the story, just telling the progression of the war as ultimately all sides start "digging in" for what was clearly going to be a war of attrition, and then attempting to turn to diplomacy to as it became clear that no side had what it took to breach the others defenses alone. The exact story going into Rebellion is unknown, but it seems after decades of all out war the previously united factions are starting to fall apart, all while the faceless threat that has chased the Vasari for millennia gets ever closer.