Your new spoiler gives information to move the plot along. It gives Magma a reason to attack Haruza and a reason for Haruza and the trainer (in case you change his name) to chase down Magam to stop them from creating a stronger Pokemon.
I know that Ho-Oh and Lugia have their feathers from the games/anime. (The silver feather from Lugia is actually a big item to move my own fics' plot along.) You could maybe make use of the Red, Blue, and Jade Orbs (the summoning items in the games) for Groudon, Kyogre, and Rayquaza for their DNA. The orbs are said to contain an ancient power, and they summon the respective Pokemon (and possibly control them which I think happens in the anime?). Magma (and maybe Aqua) could go after those items.
I think you've got enough to get the beginning written out. Good luck!