Ha looks like you finally found the way. "That's crazy!" Haha I love how you missed the point of that upgrade.
Man, you took forever to try out the diffusion missiles. Also it's totally possible to go the long way back without getting diffusion missiles but it requires a super long chain of complex speed booster jumps, accomplishing it will unlock special dialog with the computer. http://www.metroid2002.com/fusion/other_secret_message.php
I was pretty sure you couldn't go further this way and would need to go back to where the Diffusion Missiles are needed. Was I wrong?
I believe you need to unlock the red doors and then you can make your way to a navigation room without getting the diffusion missiles. Like I said though it requires a lot of painful speed booster maneuvering to pull off. There is a video on the page I linked to showing just how painful it is to accomplish. You need to maintain a Shine Spark from a certain location (Through multiple rooms) until you reach the area with the speed booster blocks that normally prevent you from escaping without getting diffusion missiles.
According to this page (see bottom of the page), you still need the Diffusion Missile in order to actually progress.
Ah I misinterpreted what you wrote, yes of course you still need the upgrade to complete the game. Getting the upgrade however prevents you from seeing the secret message!
