Back at the start
Now that you have come back to the start of the game where it all began, it's time to investigate one of the first doors you ever visited, door B, where you got your first key ring. In here you will find a room with a hole in the ceiling. You didn't have the Ladder at the start of the game, but you do now. Use it, and you will arrive in the floor above.
The second floor only has two rooms; the one you arrive in, and the room with an old man who informs you that this is a warp zone. It actually isn't, however, as you will not be leaving the front layer at all, you merely climbed into the attic.
In addition to tough armored foes in the attic, you will also find out where the one and only Ma Fratelli has been hiding out all this time. Despite her age, she is quite agile and has a fondness for tossing bombs around the house just to stop you. From your entry through Door S, you can head right in order to examine Door A before proceeding up the ladder to the section above.
In this solitary room, you will find what is mostly likely going to be the last safe you ever find. You may be tempted to use one of your keys to learn the secrets that it holds, but it really is not worth it. Highlight the space between the parentheses to read what it says (IT'S FUN TO PLAY THE GOONIES 2.) Save your keys and head back outside.
Run back to the left and make your way to the top platforms where you can climb a ladder to the upper portion of the attic. When you arrive, head left to visit Door B, or go right to visit Door C which will transport you to the back layer.
When you enter the room, you will immediately see a crack in the ceiling above. Use your Ladder to climb up through the crack, only to discover an old woman who is complaining about needing her glasses. The Fratelli hideout may begin to seem more and more like an old age home. Head back down and out to the attic, and run right to Door C.
The man standing here informs you that you have found a Warp Zone. Pass through the doors to move from the front layer to the back layer.
The back layer
Your trip to the back layer takes you to an unexplored region of the Fratelli house. The Fratelli gang will be out in force in this section, with more Fratellis appearing on the screen sometimes than you thought possible. From where you arrive through Door C, you can visit Door D to your left, and Door E to your right. Door D can be a little tricky to reach unless you are wearing the Speed Shoes. You should have them so definitely put them on before attempting to cross the gap with the low overhang.
When you first arrive here, you will notice a door to the left. If you take the door, you will enter a pitch black room. After lighting the candle, you will notice that the room is empty. Nothing you try will reveal anything. However, if you return to the starting room and try putting on your glasses, this will reveal a hole in the floor. Use your Ladder to access the room below the hole and you will find the final Fire Box, free for the taking. This will max out your Molotov Cocktail capacity at 20. Then climb back up and return to the hideout.
Another single chamber door will allow you to traverse between the front layer and the back layer. Although the room starts out pitch black, you can light it up with a Candle. The door that you just passed through is apparently hidden from sight until you use a Hammer. Ultimately, however, all you need to do to continue is to go down.
The final stretch
You arrive near the top through Door E. You will start moving to the left while descending deeper and deeper into the hideout as you proceed. The sections here are short with should prevent any major build up of enemies if you proceed quickly. Once you make it to the end of the stretch, you will find two doors, Door F on the bottom and Door G on the top.
It will take a little bit of work to fully explore this chamber which will result in the discovery of very little worthwhile. After using the Hammer to create a hole in the floor, using the Ladder to climb down, lighting the Candle and passing through the left door, and using the Ladder once more to climb down even further, all you will find is another woman complaining about her glasses. You're best off ignoring this door and heading straight to Door G.
A little work is all it will take to get you going on the right path. From the room that you enter, pass through the left door. If you like, use your Candle to light up the room, which will appear empty. Take a Hammer to the back wall to expose a door, and pass through it to return to the back layer.
You will find yourself in the small segment of the map illustrated above with doors G and H. You will arrive through door G and must navigate a small pathway to reach door H.
Entrance through this door will reveal another Warp Zone, this time with a water filled hole in the floor. Time to don your diving suit again and hop in.
Jumping into the water, you will find yourself in the small water segment illustrated on the previous map with doors H and I. This is the small section of water that you could see while rescuing the 4th Goonie, but could not access. There's nothing left to do but to swim down to Door I and complete the game.
In here, you will find a special kind of gate blocking the contents of the room beyond. You'll need a key to open it. If for some reason, you do not have a key, you can throw on the Diving Suit to return to the water, and return to a place in the hideout where you can collect keys from defeated enemies. Otherwise, open the gate with a key to rescue Annie and complete the game. Congratulations.