There is a hidden Easter egg scene here, but it involves pulling off arguably the most bananas Shinespark puzzle sequence in all of Metroid. To view this hidden scene, you must do this sequence after unlocking the Red Locks, but before grabbing the Diffusion Missiles. The trick will be keeping your Shinespark – it’s key to remember that if you start flying but fly into a slope, you’ll start running again, allowing you to crouch and recharge your Shinespark. Also worth knowing, if ANY enemy hits you, your Shinespark will be gone. A good idea is to hold a charged shot – this will make any spin jumps you perform turn into a pseudo-Screw Attack, which will kill any weak enemies.
To start, get yourself to the hallway above the Lock Room with the two mini-Draygon’s. Start running towards the left of this room and charge up your Shinespark. Lay a Power Bomb to break the blocks of the floor, fly to the right, crouch and charge, and drop down. Fly to the right and you’ll start running right away; as soon as you get into the next room, get ready to crouch. Shoot the red door open and spin jump across.
Run into the next room, and drop slightly down so that you’re not in line with either the door OR the floor and start flying. You’ll start running when you hit the glass tube. Crouch once you get towards the end of the tube – watch out for fish! They can easily bump you here. Get down to the floor, shoot the door open, and fly. You’ll start running into the next room. This is where it gets hard.
One thing to note in this room – the ground is sloped, so you can easily fly/run/crouch here. Jump upwards and land on the righthand ledge. and destroy the fish, either with a Power Bomb, beams, pseudo-Screw Attack, whatever (I prefer dropping Power Bombs myself). Fly to the right and quickly crouch. Jump over the other ledge now on the left. Though the metal block and grass area may look like different levels, it’s actually a slope, so quickly fly/run/crouch. Keep laying Power Bombs any time you see a fish move. Jump up and over into the righthand ledge and quickly get yourself into the little circular nook. Fly/run/crouch towards the left. Quickly jump up and over to the next ledge where the door on your right is. Lay Power Bombs, and fly/run/crouch up the slope in front of the door. Jump up to one more ledge, fly/run/crouch, lay Power Bombs, and go through the door on your left. Get into this next room, jump, and release your Shinespark through the top wall.
Let me repeat that: you need to Shinespark through the top half of the wall. Do not Shinespark straight through when you open the door. And for the love of all things holy, make sure you don’t accidentally release your Shinespark when jumping up to get higher. You’ll go crashing through the bricks and into Sector 4. Phew. From here, make your way back to the Navigation Room. Congratulations!
Once you arrive, the hidden scene will play out as follows.
ADAM: Samus, I’m impressed that you were able to make it back. That trick with the Shinespark was truly… ingenious.
MYSTERIOUS MAN: That’s our Samus Aran! Truly magnificent! As a reward, let’s fill her in on our plan. Hmm, computer?
ADAM: That is… not advisable.
MYSTERIOUS MAN: Bah…
ADAM: No more joking. Samus, get back on task. Is your objective clear? I wonder how many players will see this message…?