In the conventional understanding, both land and sea lay beneath the sky's embrace, so Rayquaza's sky was inherently more formidable than Groudon's earth and Kyogre's ocean.
Rayquaza stopping Groudon and Kyogre's battle was also the sky suppressing the earth and sea.
But to the true Rayquaza—
Groudon and Kyogre's conflict was merely childish squabbling.
After all, Rayquaza, which lived beyond the atmosphere, could not only see the planet below but also the vast, boundless universe beyond it. It knew that Groudon and Kyogre's fight amounted to nothing.
The difference in perspective created an imbalance in strength.
It could also be called Rayquaza's Dimensional Reduction Strike against Groudon and Kyogre.
To Groudon and Kyogre, they were fighting over ownership of the world. But in Rayquaza's eyes, it was just two idiots playing house.
As for why Rayquaza stopped Groudon and Kyogre...
"Roar~ Roar roar~"
At Mark's question, Rayquaza did not hide anything and directly gave him the answer.
The reason was unexpectedly simple and straightforward.
It was not a personal grudge like when Rayquaza beat up Jirachi, nor was it some subjective emotion or simple dislike of those two idiots, Groudon and Kyogre. It was solely because of territory.
From the ground all the way to Outer Space, everything fell within Rayquaza's territory.
Rayquaza had always been satisfied with its territory and did not want it to change, so whenever Groudon and Kyogre fought, it stopped them.
Whether there was more land or more water on the planet's surface, it would affect the atmosphere.
To keep the atmosphere from changing, it stopped Groudon and Kyogre.
"Roar~"
At Mark's continued questioning, Rayquaza gave another answer.
As for why it had landed on the planet's surface now—
Strictly speaking, this was Groudon's territory, and it should not have landed here casually, or Groudon