Wait, what's the question?

How he got to the top of the pyramid and won the prize when Onaga carried him off into the horizon, right?

Correct. Although I wanted to add my wicked humor to this, here lies a real question. I wonder what precisely happened between the situation when Onaga took Kahn to a flight (MKA) and Kahn smacking Raiden (MK9).
A friend of mine asked this a month ago and said that "So it boiled down to Raiden and Kahn surprisingly. What if someone would have just thrown a boomerang in Kahn's head? Would it be completely different now?"
Could the MKOmmunity imagine and come up with a decent solution, since we didn't get a biography of Shao Kahn to read about this?

Well, when being carried by a big winged creature, you can try to climb on top or grab them by the legs and steer them to fly the way you want, if you're strong enough.

The other possibility is no one else could beat Blaze in a fight so he had plenty of time to kill Onaga and walk back.

I've always assumed that the intro of Armageddon wasn't actually canon and that it was just the vision that Delia had. I certainly like to think that some of those characters didn't go out like chumps as they did in the intro.



I want to see this in action.

Well, the corpses on the steps of the pyramid at the beginning of 9 are pretty much laying in all the same places where those characters were in the MKA intro. I'm gonna go out on a limb and say that's not a coincidence.

Shang Tsung and Shao Kahn have their little fight. Then Onaga carries him away. While Liu Kang and Shang Tsung fight, Onaga tries to kill Shao Kahn, but Shao Kahn beats Onaga while he is preoccupied with flying. Shang Tsung dies of old age (his youth gets drained) and Liu Kang's body shuts down afterwards having no purpose left. Sub-Zero kills Scorpion, Kung Lao kills Baraka and Shinnok kills Kung Lao, Sonya and Johnny Cage get killed by someone with a sword (maybe Scorpion based on his fatalities in MK9). Basically everyone kills each other. Then Shao Kahn, having killed Onaga, makes his way back and starts power smashing through everyone who's left until he gets to the top of the pyramid. Raiden is on his trail. Meanwhile, Taven, who was originally meant to win, is about to beat blaze. Shao Kahn picks up his hammer and smashes Taven's skull in and throws him off the pyramid. Then he finishes Blaze and takes the godly power for himself. Raiden gets to the top but it's too late. He's no match for Shao Kahn at this point.

Not all of them, Sonya died in the first steps of the pyramid, and Scorpion was just behind Tsung at the end of MKA's intro and in MK9 he was far away fro there. I really think MKA's intro is just Delia's vision.

She was pushed off the steps by Johnny, I don't recall where she lands even being visible.

Darn. I just remembered – the developers did tell that while the Konquest of Armageddon is canon, the opening cut-scene is not. Konquest ended to the part where Taven was entering the big fight, proving that there was going to be one, but how exactly would it happen was uncertain.
This was probably just Vogel's way to cancel the deaths shown in the intro because he didn't know where the story was leading at next. A reason why the MK9 intro is that similar (though not 100% compatible) with the MKA intro might be that the developers didn't want the most of the players to raise an eyebrow for the sudden changes in what is canon.
It really makes one wonder; would Shao Kahn have what it takes to outsmart Onaga once again? This time in real Mortal Kombat. It would've felt better if the Dragon King were against Raiden in the MK9 intro though the intro wouldn't have connected to the later Story Mode well anymore.

It's a decent theory. But Raiden is lightning fast, right? Or is this just one of those "don't ask" things where logic doesn't prevail, e.g. Smoke's death?