Own Alone II: Win In Space City - Complete mission with empty Auxiliary Bays. - 4000 Plex.
Half Human Intuition - Defeat more enemies and structures than Nero. - 2000 Plex.
Tough Customer - Complete mission in under 420 seconds. - 2000 Plex.
An Agitant Gunboat will show up partway through, and more Valarians will arrive once you're almost done with the bases.