Legendary

Note: All wild Legendary encounters will spawn at level 85. The spawn rate for Legendaries are 1/125k without GM, With GM you have a 50% increase on the encounter rate. It is not possible to run from Legendary Pokemon.

Bad luck protection has been added for Legendaries, Your legendary encounter rate will increase the more encounters you have without encountering a legendary, this boost starts taking effect once you have around 100,000 encounters without a legendary,  and will slowly increase eg 100k, 125k,150k ... etc. The cap is 600k where the rate would be even more then a extremely rare pokemon. It will reset once you encounter a legendary
Remember, this boost only applies if you're hunting a legendary so if no legendary is found on a map you are grinding on, the number will stay the same until you grind on a map a legendary can be found. You can check how many encounters you have since your last legendary encounter by typing /lle

Articuno can be encountered in Seafoam Islands F1, Seafoam Islands F2, Seafoam Islands F3, and Seafoam Islands F4, when your leading pokemon is alive and holding a Feather of Articuno. This feather can be dropped from any pokemon on the same aforementioned maps, when your leading pokemon is alive and an ice-type.

Moltres can be encountered on Mt Ember and Mt Silver Cave when your leading Pokemon is alive and holding a Feather of Moltres, do check map names on the top right of the screen, Mt Silver Cave is not the whole of Mt Silver. This feather can be dropped from any pokemon on the same aforementioned maps, when your leading pokemon is alive and a fire-type.

Zapdos can be encountered in the Power Plant basement when your leading pokemon is alive and holding a Feather of Zapdos. This feather can be dropped from any pokemon on the same aforementioned maps, when your leading pokemon is alive and is an electric-type. You need all Kanto and Johto badges to enter the Power Plant basement.

The drop rate on the feathers are 1/9000

To confirm you have a chance at encountering one of these legendaries, type /pokemon and make sure they're on the list under the "Legendary" category.

All enhanced items increase the encounter rate by 20% when your lead Pokémon is alive and holding it.

Feathers do not disappear once you encounter the legendaries.

Zapdos, Moltres and Articuno can also be found in N Castle within Unova. You do not need the feather to hunt them there although you are able to use the enhanced feathers to boost the encounter rates.

Raikou can be found within Mossy cave, in the Thunder Cavern.
Suicune can be found within Mossy cave, in the Water Cavern.
Entei can be found within Mossy cave, in the Fire Cavern.

To find where Latios and Latias can be found, you'll need to beat Hoenn E4. Once you have defeated the Hoenn E4 you will receive an Eon ticket, which shows you where each legendary is currently located by double clicking the Eon Ticket. They are limited to Hoenn maps so they won't appear in Kanto nor Johto. The spawn area will also change daily at 0:00 UTC.
Latios and Latias can be encountered on land and in water when surfing.
If you've already defeated the Hoenn Elite Four before, you'll have to beat it again to get the Eon Ticket.
Wild Latios no longer has Memento.

You can craft a Soul Shard Enhanced to increase the spawn rate for Latios/Latias.

Altering Cave now has a 10% chance to spawn one of the following legendares: Moltres, Articuno, Zapdos, Raikou, Entei, Suicune, Regirock, Regice, Registeel, Shaymin

Mew is now accessible to hunt for on PPO. You must first obtain the Old Sea Map from the Elite Shop. Said map costs 125 Elite Tokens to be able to be purchased. Once you have the item, you go to any ferry, click the "Hoenn" tab then click on Faraway Island. Ferry trip costs 50k. There are 12 areas in total and Mew will change its location daily.

Shaymin can be encountered at Flower Paradise

To access all 3 of these areas named below, you need to of beaten the Sinnoh E4.

Heatran can be encountered on Stark Mountain maps
Darkrai can be encountered in Deep New Moon Island
Cresselia can be encountered in Deep Full Moon Island

To find where Uxie, Mespirit and Azelf can be found, you'll need to beat Sinnoh E4. Once you have defeated the Sinnoh E4 you will receive an Lunar ticket, which shows you where each legendary is currently located by double clicking the Lunar Ticket. They are limited to Sinnoh maps so they won't appear in any other region. The spawn area will also change daily at 0:00 UTC.
They can be encountered on land and in water when surfing.
If you've already defeated the Sinnoh Elite Four before, you'll have to beat it again to get the Lunar Ticket.
wild Uxie and Azelf will no longer have Memento or Explosion

Manaphy can be encountered by fishing in the Water Temple.

Deoxys is available in the PVP prize shop

Celebi is available during the Easter Event

Cobalion is available in the Battle Tower prize shop and PVP prize shop

Hoopa (Confined) is available in the Battle Tower prize shop and BQ prize shop

Jirachi Is available in the Philanthropist Points shop.

Keldeo is available in the CW prize shop.

Kyurem (Normal) is available in the CW prize shop.

Meloetta Is available from a Pokemon Box. It has a 1% chance of appearing

Terrakion is available in the BQ prize shop

Victini is available in the BQ prize shop.

Virizion Is available from the Elite Prize shop.

Volcanion is available during Summer Event

Xerneas is available during the Christmas Event.

Yveltal is available during Halloween Event

Zygarde Is available from the Battle Tower Prize shop

Giratina can only be received from an egg by placing 1st/2nd or 3rd to have a chance to get it during halloween event

Regirock, Regice, and Registeel have a chance to be encountered from any mining rock as long as your mining level is 75 or higher. These have a base encounter rate of 1/75k, this rate is checked per rock.

Regigigas is available from a Legendary egg which is an untradeable item.

Legendary Eggs - The top 3 players who deal the most damage in World Boss battles have a 15%/10%/5% chance to get the Legendary Egg that contains the respective world boss legendary pokemon. You can also get the Eggs as PVP Tournament prizes.  The pokemon available are Articuno, Azelf, Cresselia, Darkrai, Entei, Heatran, Latias, Latios, Mesprit, Moltres, Mew, Raikou, Regigigas, Shaymin, Suicune, Uxie, Zapdos.

Cherish Ball - Has the chance to contain one of the following Legendaries: Articuno, Moltres, Zapdos, Suicune, Entei, Raikou, Regice, Regirock, Registeel, Xerneas, Celebi, Yveltal, Volcanion (note these will be level 40, not 3)