|His yellow "tattoos" now|
float beside him like ribbons.
One Pokémon looked down upon this battle from the sky above. The Pokémon that dances in the heavens: Rayquaza. Rayquaza is venerated by the people of Hoenn as their protector and savior. When Primal Groudon and Primal Kyogre had battled for 20 dawns and 20 nights, the world began to lose its natural balance and tilt toward destruction. The people, unable to endure any more, cried out to their mighty savior Rayquaza before a great stone that shone with rainbow brilliance. And a change came upon Rayquaza, weaving in the sky above Primal Groudon and Primal Kyogre. Suffused in brilliant light, its body began to transform visibly. And then..."
This shows that unlike the other two, Rayquaza mega evolved at the request of humans (with the "great stone [...] with rainbow brilliance" likely being a giant Keystone). Mega Rayquaza gets the new weather ability Delta Stream. This ability overwrites any currently in effect weather as well as blocks weather moves (like Sunny Day) and weaker weather abilities (like Drought). The new weather type also reduces damage from moves on Flying pokémon to normal damage. The weather is removed if Desolate Land or Primordial Sea is activated second or if Mega Rayquaza is switched out. It also learns a new flying move, Dragon Ascent, which is likely a variant of Overheat.