The second part where it scans for 6 minutes, tells you to kill 2 assaults, collect the scrap metal from one, then return to station. We killed all of the assaults, I picked up scrap metal, waited for the obscenely long countdown, and... nothing. Waited 5+ minutes after and nothing. When I leave the sector, it fails the mission.

PS: h8 u phaserlight

You have to destroy the bots yourself on this mission. There is a video tutorial on how to pass it here.