You'll wake up in what you're told is the dump of the island, where all the trash gets sent. Take that "never get free" as a challenge and start to climb upwards taking out the annoying purple blobs.
Reach the top and interact with this computer console to open up the door down the bottom. For a little bit of fun, see if you can fall all the way down to the ground without hitting any of the floating platforms!
Make your way through a few more sliding blocks and you'll get into the real meat of this place, Bug Soldiers and all. Although the ones inside this little building here are friendly.
In fact, the store clerk inside offers a nice proposition, if you let him look at your Polar Star and Fireball, he'll combine the two weapons into the Snake, a short ranged weapon that can penetrate walls. I'd personally save the Polar Star for the third and final trade offer soon.
Not much further along you'll bump into two frogs that were ran out of their clinic and Curly brace who got sent here as well. Talk to the Doctor to be healed up, and given the side quest to fetch some medicine from the clinic. Not sure, but this might be needed if you're going for the Best End.
Regardless of what you do, continue on afterwards through some tricky sliding block bits.
You'll be quickly arena trapped in with a mechanical boss that zooms across the plain back and forth before settling and launching attacks at you.
When it does settle to attack, it'll open up, showing its weak spots to you. Before you are able to do any damage to the boss, you'll need to shoot all of the green spots when it's open. Once they're all gone, you can hurt the boss by attacking the inside while it's open.
Due to the high firerate and close proximity, the Level 2 (NOT Level 3) Sword completely destroys this boss. Get in close and deal as much damage as you can, while trying not to get levelled up to 3 or down to 1.
In the room after the Boss, you'll see Prof. Booster be teleported in and fall down into a pretty deep hole. WARNING! SAVE BEFORE DOING ANYTHING ELSE! If you're going for the Best End, Jump over the gap without going down to check on the Prof., you'll ruin your ending if you do. Use the Red Line to make sure you make the jump. If you don't care about getting the best ending, jump down to check on Booster and get a pretty cool Jetpack!
In the next room, when trying to move the boulder you keep hearing mentioned, Balrog will come down and try and fight you. This time he has a bad habit of jumping up high and unleashing a storm of missiles.
Manage to defeat him again, and he'll agree to help you move the boulder out of the way so you can continue.
Behind the massive boulder, you'll be entering the Deep Labyrinth. It's primarily a ton of combat, so keep on your toes against some powerful enemies, and you'll make it through fine.
Part way in, you'll find a teleporter that will take you back to the Bug shop if you wanted to grab the Snake and didn't before, but be careful! If you jump down without the Booster v0.8 you're going to have to take the LOOONG way back!
Make it through that combat fest into this nice resting area. Save up and follow Curly into the door.
To make it through these blast doors, first open them at the console just above, shoot the faulty door until it opens, go back to the first console, then swim underneath and use the second console. Save afterwards, trust me.
If you're going for the Best End, find the Tow Rope in the waters below in the next room BEFORE talking to curly. Otherwise, go straight for her. After a small cutscene, a boss fight will start against…
The Heart of the Island! This is one mean boss, especially seeing as the water will rise up commonly making dodging quite a pain. You deal damage to the boss by hitting the Main Core when its blue eyes are showing.
Make dodging and outlasting this boss your focus, while trying to deal as much damage as you can when given the window.
Just as you're about to put this Core down for good, Misery will come rushing in after realizing her mistake. If the core dies, the Island will crash down into the ground! By the orders of the Doctor, Misery will run off with the core to preserve the Island, and the room will flood.
You'll run out of air and die… or will you? After you run out of air and black out, she'll remove her Water bubble and give it to you, saving you but not herself. If you're going for the Best End you would have seen some extra text when you fainted. Don't forget to use the Tow Rope.
Make your way back to the Dark Place and enter the now-open Tiger Mouth into the Living Waterway.