I can say that it’s unfair for two Deoxys to fight against one Rayquaza. If you watched the entire movie you must have known that Rayquaza is still alive despite all the damage. To be honest, all main character in Pokemon are destined to never die (since the majority of audiences are children and they expect happy ending), as shown in Darkrai movie.

My seven year old Pokemon fan says Rayquaza fainted, because Pokemon don’t die.

Of course, to me that doesn’t explain Pokemon fossils or Cubone’s mother…