Alright cool. The way I see it right now, The Congregation and the Builder come out of slipspace and into SF territory, the Builder tries to create the Xurs (guardianships) to guard the Congregation while they communicate with the Federation, but the SF pick up the hardlight manipulation before the Xurs actually form, with their advanced sensors and fire at the Builder, destroying his suit (though his consciousness is still in tact), The Congregation retreats a few AU away from the planet, recreate the Builder's suit, and comes back to invade the SF's outer rim of planets.

Sound good? :D