It's easy to get caught up in the "me against the baddies" mindset -- as Levi says, "I'm here to take down Grax and the Legion single-handed." But the Expedition and especially the Prospectors can be very helpful. You can be in only one place at one time, but by Act 4 the Legion is starting to press forward on multiple planets simultaneously and armored outlaws are popping up everywhere. The locals can't do it all for themselves, but if properly equipped they can significantly slow the enemy's advance on their planet.

In some cases (probably at higher difficulty levels), having strong local forces may actually be necessary. I've seen a few reports from players that Legion or Sloop Tanks have wiped out the Prospector Guard at some of the ruins they'd previously liberated. Apparently there's no way to re-liberate a prison. If you lose one of those, you'll never be able to reach 100% completion on that planet.

Here are some things you can do to help the planets inhabitants fend for themselves:
  1. Enlist, build, and upgrade armories. That one's pretty obvious.
  2. Haul defensive turrets from armories to locations you think need extra defense. Those turrets are surprisingly capable.
  3. Provide samples of corrupt Nova to the armories so they can add elemental damage capabilities to their defensive turrets.
  4. Haul automenders from workshops to locations where Expedition or Prospector ships might come under fire.
  5. (Requires an Expedition pilot) Buy the Expedition Wing/Shield Projectors upgrade to the Equinox, to give energy shields to the Expedition and Prospector units.
  6. (Requires a Prospector pilot) Buy the Defensive Ops/Elemental Offense upgrade to the Equinox, to give elemental damage capabilities to Expedition and Prospector weapons.
  7. (Requires 10 levels among Prospector pilots) Buy the Defensive Ops/Metallurgy upgrade to the Equinox, to provide stronger armor for Expedition and Prospector units.
  8. (Requires 5 levels among Outlaw pilots) Buy the Outlaw Barracks/Pirate Assault upgrade to the Equinox, to upgrade Expedition and Prospector weapons.

Building a Starlink Tower on a planet gives a huge boost to the locals on that planet. For example, when I built a Starlink Tower on Tundria, my armory (and its vigilantes) jumped from level 19 to level 35. This is a lot harder to control, though, because you have to build one on Kirite -- thus preventing you from building one on Haven or Sonatus -- and you can only build on one planet in the the Frontier Sector and one in the Dark Sector.

There are also some ship mods that will help Expedition and Prospector units when they're assisting you in a skirmish:
  1. Alliance Core doubles the damage power of their weapons.
  2. Commander Core (except level I) increases their resistance.
  3. Tank Core increases their resistance.
  4. Alliance Armor reduces damage they receive by 10%.