After you get your fully powered suit, you can easily get past the Space Pirates in Chozodia.
Use Your New Suit
Use Space Jump to go upward through this room, to the upper right corner, where there is a tunnel. Go through it. The stones below you will move downward, blocking the entrance to the engraving. Go to the right and you will fall through Pit Blocks. Space Pirates will attack, but you can just Screw Attack through them or shoot them once to defeat them. There is no longer any need to hide from them.
Follow the path to the save room and use it to heal up and save the game. Then leave the save room through the door on the right.
Shoot the floor with missiles and fall into the water, which you can now move freely in. Go to the bottom, then go to the leftmost side, and run right to break through the Boost Blocks and get a Super Missile tank.
Shoot the block above you and make your way up the room, and go through the upper right door.
Screw Attack through the blocks on the right. Go down to the ledge just below where you entered the room, then shoot the upper block of the wall with a Missile. Go through to get a Missile Tank but don't go too far to the left or you will fall through Pit Blocks. (If this happens, just go back up through the room you fall into, to return to the tall room.) In the tall room, go down the room and defeat any Space Pirates that attack. Go down to the bottom of the room and Screw Attack through the blocks on the left, then go through the door on the left.
There is lava below, but you're safe from it with your new power suit. Screw Attack through the blocks, then fall down and to the right in the lava. Go through the tunnels on the right to get a Super Missile Tank. Go back out through the tunnels and go to the left. Make your way to the left side of the room, then go through the tunnel on the left.
Go down through the room. You don't have to worry about being seen by the eyes, but watch out for the beams they shoot. You can actually kill the eyes with your beam. Kill the Space Pirates, go down to the bottom of the room, and go through the door on the left, then go down below (it's OK if you fall through a Pit Block) and go through the door on the right.
Bomb the right wall to make the blocks disappear. There is a niche in the right side of the room where a Space Pirate is standing. Kill it, then face the left wall and shoot a Missile at it. Roll into the hole and use a bomb, then roll left to get the Super Missile Tank. Then go to the bottom left corner of the room and roll through the tunnel.
Go left and bomb or shoot the block, then roll left through the tunnel. Go to the left while shooting and you'll break through the blocks and kill the Space Pirates in the way. Keep going left to the next room.
Space Jump to the top of the room while killing Space Pirates, then go through the top left door.
Go to the bottom of the room and go through the door on the right, shoot any Space Pirates that followed you, and when the shutter opens, go through the door on the right, where you can save the game. Then go through the door on the right.
Ignore the Space Pirate in the shadows and go through the door on the right.
Shoot or bomb the block in the tunnel, then roll in the tunnel and drop a bomb to break the blocks above you. Go to the right while shooting, then go through the tunnel on the right.
Go through the tunnel and shoot the Space Pirates, then Space Jump up the room and go through the door on the right. You are now in the Space Pirate Mothership.