Oh...my...god.
Jirachi, you're a good person but this Raichu place, well, the info they gave you was 100% untrue, uless perhaps the small possible link between Jirachi and the Regis, seen below. I happen to have watched movies 1-5, seen full reviews of 6 and 7, played the game, and done some other research. Here's the real story:
Registeel, Regirock, Regice: A long time, thousands of years ago, humans (it doesn't explain how, I'm guessing a magical seremony or whatever, or possibly using a wish from Jirachi) created the Rigis. However they were too powerful, and needed to be sealed away (again maybe they wished for Jirachi to seal them, see Note at bottom). There they stayed that way until they were captured in Ruby/Sapphire.
Jirachi: Jirachi has nothing at all to do with Deoxys, Latios, Latias or Rayquaza. It just grants wishes every 1000 years. The whole how it exists thing may be that it's just been around for eternity, like Zapdos, Articuno and Moltres, for example. Or Mew.
Rayquaza: For those who have played Ruby/Sapphire, Rayquaza was the one who put Groudon and Kyogre to sleep in order to stop the cataclysmic battle between them. I don't know why, but in the 7th movie, it has a dislike for Deoxys, trying to destroy it every time it shows up.
Latios and Latias: In the 5th movie, it clearly states that the father of Latios and Latias was indeed another Latios, proving that Latios and Latias were and have always been pokemon. The movie also says that they have the ability to take on the appearance of someone else, usually a human in order to avoid detection.
Finally, we reach what seems to be the most controversial pokemon here.
Deoxys: As the pokedex entries state, it was a deep space virus floating around. It was hit by a laser, (I don't ever remember it saying that it was a laser from a sattelite) transforming it into its current state. Like Mewtwo, its overly superior intellect caused it to believe that everyone else was inferior and to be destroyed. then it came down on an asteroid to appear in the 7th movie.
Note:In the 6th movie, Masato/Max wishes for candy, chips and stuff from Jirachi. Jirachi grants the wish, but just teleports it from a nearby stand (most of the movie takes place around a carnival). If it is true that the humans wished for Jirachi to seal them, it would make sense because Jirachi could teleport them to a sealed cave.
Well, there it is.
