Thank you for all the help from you guys especially @lostaddict, @BlackShark, @suloku and everyone who contributed their Mystery Events and Mystery Gifts.
Now it's about time to share everything we have learned from the research. Mystery Event Activation RS: Section 2 - 0x03A9 - bit 5 RS: Section 2 - 0x05C0 - bit 1 (Flag for the NPC?) E: Section 2 - 0x0405 - bit 5
In Ruby & Sapphire Mystery Event can be activated by the NPC at the 1F of the Pokemon Centerin Petalb