I wrote this guide in 10 minutes because I feel that a game this good is way too obscure. I couldn't find any of this online, so I've decided to beat the game and write a guide myself.
When I find the necessary time I'll improve the formatting, add some images, and maybe write in detail where each item can be found. Until then just remember that a poor guide is better than no guide at all. Enjoy.

Should unlock along the way.
Should unlock along the way. If you're so good you never die: Save. Get killed. Reload. Repeat 20 times.

For this ending you need to:
1. Destroy the big guns (cannons) in the Missile Base.
2. Fully upgrade the radio. You'll need:

• Computer Unit
  
• Long Metal Rod
  
• Warp Coil

3. Enter the Communications Array via a teleporter in the Ship Cemetery.
4. Find a spot with marines and turrets. Use your radio there.
5. Survive the standoff.
For this ending you need to:
1. Fully repair the escape pod and carry it all the way to the VC Base located in the Mining Field.
2. To repair the escape pod you'll need:

• Navigation System: Star Chart + Modded Subscape Radio
  
• Propulsion System: Warp Coil + Particle Accelerator + Fuel Cell
  
• Life Support System: Life Support Chip (found in Ship Cemetery and Eden) + Specimen Container + Replicator Cell

For this ending you need to:
1. Infiltrate the VC Base located in the Mining Field to find the key to the shuttle.
2. Take the shuttle to a new location.
3. Destroy all round things to open a new path.
4. Kill two VC Commanders in the newly opened area.
For this ending you need to:
1. Kill all alien queens in The Hive area.
2. Destroy all eggs in the queens' nests.
For this ending you need to:
1. Kill unique enemies in Eden: one of them is a larger version of those fast monsters you may encounter in this area. It drops the Planetoid key item.
2. Kill all remaining vines in Eden: they're in the middle of square zones made of stone.
3. Bring the Planetoid to the most distinctive one, use it there.
4. Survive the standoff.
For this ending you need to:
1. Go to the Mining Field.
2. Find or craft a Welding Torch (Glass Tube + Lighter, both found in the Mining Field)
3. Find and open a large crate with the Welding Torch to find the Tattered Paper.
4. Combine the Tattered Paper with the following items, in the following order:

• 1. Sniper Pistol = Pistol + Long Metal Rod
  
• 2. Beacon Ray = Radiator + Pulse Beacon (drop an unlit beacon then pick it up)
  
• 3. Rapid Fire Pistol = Cooling Unit (Glass tube + Ice pack, both found in the Mining Field) + Pistol
  
• 4. Propulsion Boots - found in another large crate in the Mining Field
  
• 5. Flame Thrower - drops from flamethrower marines in the Mining Field.
  
• 6. VC Stun Laser - drops from stun laser marines in the Mining Field.
  
• 7. VC Pistol - drops from rapid firing marines in the Mining Field.
  
• 8. Electro Sphere - inside the Security Box, which is dropped by one of the marines. The Security Box can be opened with a Security Card, also dropped by marines.
  
• 9. Reaper Corpse - drops from reapers (duh) most commonly found in the Hive.

5. Use the newly created Glowing Paper.

Find a force field generator in the Missile Base area. Place it inside the hermit's hut and close the door. Simply stay inside the force field for 100 days - your health and food will regenerate.