If I remember correctly, the Contest only gives you a Sun Stone until you beat the Elite Four. After that, it should give you all elemental stones randomly (I don't think it can award you an Everstone, though... I don't really remember...)
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Spoilers below. If you're playing the game for the first time, please refrain from looking at these.
Back when PokéUE was still on Game Jolt, it had trophies for finding the easter eggs:
D'aww: The Pikachu loves you!
Let It Go: Let it go, let it go, turn away and slam the door, I don't care what they're going to say. Let the storm rage on; the cold never bothered me anyway.
Ghost Ship: Who turned the lights off?
Playtime Is Ogre: find the "A Cold Night" story
Pervert: Talk to Erika or Sabrina while wearing the Nude "Outfit".
Thief: Steal the last Pokéball from Oak's lab.
Cervix Crusader: Rape Misty.
I think they could serve as good hints. :)
And as for the legendaries, there are a lot:
Celebi: I think Celebi was a 0.3 exclusive Pokémon. It might be available in a Mystery Gift. I don't remember... You can obtain it by holding a GS Ball and interacting with a statue in the Forest Ruins (I think that's what the place was called, it's been a long time...). If you're using Debug mode, you can add GS Ball into your inventory.
Regice: Seafoam Islands
Regirock: Victory Road
Registeel: Moonside Lake
Regigigas: Mt. Moon
Ho-Oh: South Amber Road
Lugia: The Dead End (I think...)
Articuno (Roaming, more info below)
Zapdos (Roaming, more info below)
Moltres (Roaming, more info below)
Latias: Trainer Tower
Latios: Trainer Tower
Cobalion: I don't remember, sorry
Terrakion: I don't remember, sorry
Virizion: I don't remember, sorry
Keldeo: I don't remember, sorry
Entei (Roaming, more info below)
Raikou (Roaming, more info below)
Suicune (Roaming, more info below)
Deoxys: I don't remember, sorry (An exclusive item may be required)
Mew: I don't remember, sorry (An exclusive item may be required)
Mewtwo: I don't remember, sorry (An exclusive item may be required)
Arceus: Mallet Town :)
Pokémon start roaming after the champion is defeated
Route 18 -> Route 19
Route 19 -> Sea Route 20
Sea Route 20 -> Route 21 or Sea Route 22
Sea Route 22 -> The Dead End or Sea Route 20
The Dead End -> Sea Route 22
Route 21 -> Runko Harbor
Runko Harbor -> Route 18
Route 2 -> Route 3
Route 3 -> Fucksia Woods
Fucksia Woods -> Route 8
Route 8 -> Route 14 or Route 3
Route 14 -> Route 15
Route 15 -> Route 16
Route 16 -> Route 17
Route 17 -> Route 2
Route 4 -> Route 5
Route 5 -> Route 6
Route 6 -> Route 23 or Route 7
Route 23 -> Route 6
Route 7 -> Route 11
Route 11 -> Route 9
Route 9 -> Route 4
Pokémon start roaming after Final Cave is cleared
(Western Runkku Islands)
Chroma Road -> Chroma Cave or Indigo Path
Chroma Cave -> Chroma Road
Indigo Path -> Victory Road (Outside) or Victory Road (Cave 1) or Victory Road (Cave 2)
Victory Road (Outside) -> Victory Road (Cave 1) or Victory Road (Cave 2) or Chroma Road
Victory Road (Cave 1) -> Victory Road (Outside) or Victory Road (Cave 2)
Victory Road (Cave 2) -> Victory Road (Outside) or Victory Road (Cave 1)
(Central Runkku Islands)
South Amber Route
North Amber Route
East Amber Route
(Moves through these four at random)
(Eastern Runkku Islands)
East Amber Route
(Moves through these four at random)
Hope these will help you completionists!
3D Pokémon fan game? I am not working on such thing. And no, I'm not planning on updating PokéUE. I released the source so that people can fix the game themselves if they want to. I've moved on to other things. And thank you... hearing people call something a masterpiece feels very nice... but I don't think the game's a masterpiece.....
Hey, I think I remember your name. I did indeed finish PokéUE and I've been in college. I kind of want to make another Pokémon fangame but I know that it will be taken down by Nintendo. Right now I'm just studying and procrastinating. No big projects.
It's been a year since I finished 1.0. To celebrate, I've decided to release the source publicly. I won't be updating the game anymore, so if you know how to use RPG Maker XP and Pokémon Essentials, you can make your own patches and share them!
I know this is a source for a silly fangame but I hope
you will respect these.
1. You can not make your own fangame out of this. Use it to
see how things are done, maybe you'll learn something. Also, don't
take any assets from this fangame for your own. Pretty much none of them are mine.
2. Feel free to make your own patches for Pokémon Uncensored Edition
with this! As long as you don't distribute it as its own game,
it's fine. And as an added note, it'd be cool if you put it up on
the game's discussion boards at itch.io. I'd love to see what you
can come up with!
3. That's pretty much it! That wasn't so bad, was it?
I'm glad you liked the game. The post-game content will double your playtime if you want to 100% it (and it takes ~100hrs to 100% the game. Yes, there are people who have done it). Do keep in mind though that the Post-Game story chapters are pretty crazy... it turns into some sort of psychological horror for a while. No jumpscares or anything like that, just some really weird stuff.
I haven't been paying attention to this game at all; there's some bugs and other things I need to fix but after the game was semi-DMCA'd I've lost all motivation. Might do that stuff soon.
I'm pretty certain you can find all the starters in the wild (except gen 1 starters) but Cyndaquil is an especially tricky one; you have to talk to the Nurse in the Dildadon City while you're playing as Purple.