When the System Alliance reach the stars they didn't meet the Citadel Council. The met the Fallen(destiny) and the Hissho(endless space) and thus started a three way war. The Council sends a scouting fleet through a Relay into unknown space and find the three factions fighting over a garden world. How is comes to past is up to you and your imagination. You can also decide how the System Alliance forms and what level technology they have. I wish you luck.
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