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A secret conversation can be witnessed in Metroid Fusion. To hear it, Samus must perform a difficult series of Shinesparks in Sector 4 after she has opened Level 4 security doors, but before she obtains the Diffusion Missiles. This process is very difficult and is a form of Sequence Breaking, one of few possible in Fusion. However, since the message is in the game, it is likely that the developers foresaw the sequence and therefore programmed Adam to direct Samus to obtain the Diffusion Missiles immediately after entering the Navigation Room, to avoid further Sequence Breaking.
An alternate method involves firing an Ice Missile on a Powamp while it is closed, achieved by Space Jumping underneath a platform and then shooting the Ice Missile diagonally down into at the creature. The Japanese version fixed this trick.
In the message, Adam is impressed by Samus's technique to skip the Diffusion Missiles. A shadowy figure presumably working for the Galactic Federation appears to congratulate her as well and wants to reward her by telling Samus about the Federation's secret program. However, Adam states this is unwise, and prevents the figure from doing so, telling Samus to continue her mission. This is foreshadowing the Metroid breeding program. Notable also is Adam's breaking the fourth wall before allowing Samus to leave.
This is the dialogue that is said once the sequence break has been accomplished.
(A shadowy figure then pops in, seemingly addressing Adam)
That's our Samus Aran! Magnificent! Truly magnificent!
As a reward, let's fill her in on our plan. Hmm, computer?
That is...not advisable.
No more joking.
Samus, get back on task.
Is your objective clear?
I wonder how many players will see this message...?
After receiving the Secret Message, if you access the Navigation Room Computer again the standard Confirm mission objective? (Yes/No) will pop up, if you choose No as your answer you will receive an extra bit of Secret Message dialogue:
(The Federation employee then pops in again, this time speaking directly to Samus)
Samus, the plan I mentioned...
(Adam intentionally interrupts the Federation employee before he can say anything else)
Samus, return to the correct route immediately.
(Note: If you choose Yes, you will read the original message again.)