First you activate the Fallen Spire Plot by selecting 'Fallen Spire' in the Game Options Tab (If I got the name wrong its the third or 4th tab, the one that mentions human resistance fighters and the like at the top)
Then after you start your game you should have a notice for a new journal entry in the upper left corner, and you can build a new ship called the survey vessel on the economics tab of your Command center. Build this survey vessel to get things started.
Just a quick tip: Let the survey vessel's timer finish before kicking the AI off any of your neighboring planets.
Enjoy your game