Once you've docked and talked on board over the comms to Noah Gaffelt, they need some time to prepare. You should stock up your weapons, and make sure you are fully repaired and equiped with scanners.

You will then get a message that they are ready, or if you hang out in front of the Temple, it will automatically start. First the ambush takes place and then it's your turn to fight. Shoot down a few of the pirates so you can easier take out the true Searcher of Light, Ion's Corvette. It takes a while for the shields to be worn out, but once they are down, he surrenders.

Watch the talk carefully and also listen very carefully to the mission briefing.