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Special Spawns

Beyond shiny and ghost Pokemon, the wild holds a handful of rare special-palette spawns. Some appear on their own; others only show up when you are carrying a specific Pokemon and are the closest player within 50 blocks of the spawn. When one spawns it is announced to the server (except in cities, dungeons, and the story regions, where these broadcasts are silenced, and the Drowned World, which only announces shiny and ghost finds), with the palette name colored to match the find.

Gold spawns

Gold Pokemon are announced in gold text.

Spawn Chance Condition
Gold Ditto 1 in 20 Any wild Ditto
Gold Muk 1 in 20 Any wild Muk (not in the dungeons)
Gold Mewtwo 1 in 3 You must have a Gold Mew in the first slot of your party

When a Gold Mewtwo triggers, you are told "The golden energy from your Mew transforms the Mewtwo!"

Meta spawns

Meta Pokemon are announced in dark green text. They chain off each other: you have to carry the earlier link to unlock the next.

Spawn Chance Condition
Meta Kyogre 1 in 10 Meta Groudon in your first party slot
Meta Rayquaza 1 in 10 Meta Groudon and Meta Kyogre in your first two party slots

Milquaza

Milquaza is a special Rayquaza. When a wild Rayquaza spawns and you are carrying a female Miltank in your first party slot, there is a 1 in 20 chance it becomes a Milquaza. The find is announced to the whole server.

Crystal Entei

A wild Entei has a 1 in 10 chance to spawn with the crystal palette. Crystal Pokemon are announced in aqua text.

Spirit spawns

Near a graveyard, a spawn can be replaced by a spirit palette Pokemon, 1 in 500 at night and 1 in 1,000 during the day, drawn from a Halloween-themed species list. Announced as "Spirit [Pokemon] appeared" in aqua.

Possessed Vigoroth

In any jungle biome, a Vigoroth can spawn with the possessed palette, 1 in 500 during the day and 1 in 1,000 at night.

Ghost spawns

Any wild Pokemon can roll the ghost palette at a base rate of 1 in 80,000, whether from normal spawns, fishing, or skill-world zones. Night improves the odds by 10%, and a graveyard at night improves them another 10%. Ghost Pokemon are announced as "Ghost [Pokemon] manifested" in purple text.

There is one more way to find a ghost: whenever you knock out a genuinely wild Pokemon (a KO, not a catch or a flee), there is a 1 in 8,000 chance its spirit lingers as a catchable ghost-palette copy at the same spot, same species, form, and level, with three guaranteed perfect IVs. This does not happen against bosses, trainers, shadow Pokemon, or raids, or inside cities, dungeons, Skyblock, Orre, or the story regions.