This Game Progression Guide will explain the steps needed to beat the game in it's current state
After building your base, place your Auto-Builder. You will need Iron and Blue Energy Gems to craft the Auto-Builder MK II. Go around the surface and kill the Blue Fireflies around the surface. You can go around in the Surface Caverns or use your scrap iron to collect the necessary Iron. Build the next tier of Auto-Builder and use your Blue Energy Gems to upgrade the Miniaturizor to the Miniaturizor MK II.
You now need to collect Red Ferns to build the Auto-Builder MK III and Coral for the Plasma Machine Gun. Red Ferns can be found to the west past The Chasm. You will need to build a bridge to get over The Chasm.
Coral can be found in very deep pools of water. If there aren't any deep pools on the surface, create your own by blocking cave openings.
Once you have built and placed Auto-Builder MK III you will now need to collect three Red Energy Gems from the Red Fireflies which can be found at the base of the Volcano to the east. This enables the upgrading the Miniaturizor MK II to the Miniaturizor MK III.
In order to create Auto-Builders for Tier 3 and 4 you will need to get Aluminum from the Stone Caverns. During the exploration in the Stone Caverns, make sure to collect enough material to get the Black Dweller Armor and the Plasma Sniper Rifle. If you happened to find a patch of Black Dirt, explore the area to get Black Grass, necessary to craft the Rocket Launcher, and Black Mushroom, necessary for the Miniaturizor MK IV. The rocket launcher is very useful for killing Black Hounds and Black Dwellers.
Strategy as of v.10
Go to the far western area of the map of the Stone Caverns. Go to the lowest spot until you start hearing different music playing. Place Heavy Turret you to help deal with the bat spawns. Wooden platforms to walk on are very useful in this fight. The sniper rifle is useful for dealing decent chunks of damage, and the laser gun's rapid rate of fire and penetrating ability make it easy to wear down the boss' health while simultaneously killing off the swarms of lesser enemies.
You will need tier 3 building materials: Reinforced Concrete Wall and Iron Support to build a tower to reach the Floating Islands. (side note: You can build a lower tower and jump to the clouds by jumping up and shooting down with the Overcharged Plasma Gun) Once you have farmed the Gas Rock build the Auto-Builder MK IV, and use black mushrooms to create Miniaturizor MK IV.
There are several materials you will need to farm here: Crystals, Light Crystals, Black Crystals, and Ant Shells. The Black Crystals will spawn rarely where the Light Crystals will normally spawn. The Armored Ant and Acid Ant will occasionally drop the Ant Shells.
Part 2 - Firefly Queen
Use the Tier 4 building materials to create a platform on the highest floating island to reach the firefly queen.
Strategy as of v.10
On the highest building platform, create the tallest tower you can (Composite Wall and Composite Metal Support) and use the Jet Pack (created from Master Gem the Firefly Queen drops) and launch yourself into the sky. You can use Overcharged Plasma Gun & Plasma Shotgun to reach Skylands.
Tip: Create a Pool of Water on the ground to either the left or right of the Floating island. What I did was launch up they, take away 2-3 blocks, then fall. I did this until I could place a platform and stand on it.