are you going to continue this story?

I'm sorry I didn't favored this sooner

Great chapter!
You f***ing bastard, Gendo! DX DX
Arceus, Please help Yui and Shiniji to escape from her cruel husband! :(
Please write more chapters! XD XD

You know, if you can't get the game, you can see walkthroughs on Youtube. Otherwise, good start.

Wow, you made Gendo even more of a douchebag. In canon, he's simply a very bad parent obsessed with her dead wife. In Campus Apocalypse, he's a definitive jerkass that still wants to revive his wife. Bash him, please.
By the way, if this is Pokémon Platinum, Giratina would be the second god-like entitie that Shinji would befriend alongside Kaworu. Will Kaworu travel to the Pokémon World to meet Shinji? Bet he and Arceus will have an interesting conversation, including their thoughts about the First Ancestral Race.
By the way, Cyrus and SEELE's plans are antagonistic against each other, though both want to become God. Cyrus wants a world without spirit while SEELE wants to evolve humanity by stuffing all human souls into a hive mind. There's no way Team Galactic and SEELE will agree on helping each other.
Can Uxie, Mesprit and Azelf convince a post-Third Impact humanity to regain individuality and restore their bodies? Or nullify AT Fields? They created the concept of spirit in their world, afterall.

Interesting the mechanic about protagonists of Pokémon media being Chosen Ones by Arceus Himself. Explains why they're so badass.
On another note, I want to see Legendaries battling Angels or Evangelions. Especially the Creation Trio, Arceus first children and gods of space, time and antimatter. Though having a kaiju fight with Primal Kyogre and Groudon in the Pokémon side will be awesome.
Evangelion may be a cosmic horror story but Pokémon is a death world that can take off its gloves if threatened and contains creatures that embody concepts or forces of nature and have planetary or universal levels of power. The Angels, SEELE, Gendo and Nerv won't know what hit them.

Awesome story with brilliant prologue! :)
Please write more chapters! XD XD
Please continue your story! :) :)