Legendary Pokemon
Legendary Pokémon are a group of incredibly rare and often very powerful Pokémon, generally featured prominently in the legends and myths of the Pokémon world. In general there is only one of each Legendary Pokémon available.
Legendaries often are related to other Legendaries as duos, trios, etc. Pokémon 3D currently has 19 Legendary Pokemon (and Phione) available.
Kanto
Legendary Birds
The three Legendary birds, also known as the Winged Mirages, are the resident Legendary trio of the Kanto region. The three are Articuno, Zapdos and Moltres. Each one is part Flying-type and either Ice-type, Electric-type and Fire-type respectively. Each of them is based on a mythical bird, and each is associated with a season (though none of the three is associated with autumn).
All three are available in the Kanto region. Articuno takes up residence in the Seafoam Islands in the south, Zapdos outside the Power Plant in the east, and Moltres in Mt. Silver in the west.
Mewtwo
Mewtwo is a catlike Psychic-type Pokémon which is an enhanced clone of the Mythical Pokémon Mew. Mewtwo has two Mega Evolutions, which increase its base stat total to 780.
Mewtwo was too powerful for its creators and escaped from the Pokémon Mansion, wrecking it in the process. Mewtwo then made its home in Cerulean Cave, where all kinds of powerful Pokémon live.
Jirachi
Jirachi is a Steel/Psychic-type Mythical Pokémon. It is said to able to grant any wishes written on the tags on its head once awake. It only wakes up for seven days once every thousand years. If in danger, it will fight without waking up.
Jirachi slumbers atop the Millennial Star Tower in northern Kanto. The tower had until recently been lost in the mountains but a recent breakthrough led to it being discovered and connected to the Saffron City Magnet train.
Johto
Legendary Beasts
Like the Legendary birds of Kanto, a second trio of similar types is found in the neighboring Johto region. These Legendary beasts, so named because their features are based on many different creatures, both real and mythical, as well as mythological deities, were trapped in the Brass Tower when it was struck by lightning and burned to the ground, resulting in their death. The trio was revived by the power of Ho-Oh and now roam across the land because of their great power. It is unknown whether the three were already a Entei, Raikou, and Suicune when they died, or whether they were simply three non-Legendary Pokémon, and Ho-Oh reincarnated them as the first Legendary beasts. In the case of the latter, it is possible that these three would be the original three beasts, who created multiple descendants. For example, a new Entei is said to be born whenever a new volcano is formed. They are Fire-type, Electric-type and Water-type respectively
Tower Duo
Lugia and Ho-Oh are a pair of Legendary birds which formerly resided in Ecruteak City atop tall towers, leading to their designation. However, when the Brass Tower, the home of Lugia, was struck by lightning and burned to the ground, they both flew away, Lugia resolving to make its new home in the Whirl Islands and Ho-Oh to search the world for a pure-hearted Trainer. The two are thought to be as closely related as they are polar opposites, being based on the eastern legends of the Fenghuang and Ryūjin.
Lugia does not play a central role in the storyline, instead being mentioned only as having lived in Ecruteak City before the Brass Tower burned. It is found in the Whirl Islands if the player holds a Silver Wing. It is a Psychic/Flying-type.
Ho-Oh has a much greater focus during the storyline, being named as the creator of the Legendary beasts. It can be found, if the player has a Rainbow Wing, atop the Tin Tower. It is a Fire/Flying-type.
Celebi
Celebi is a Psychic/Grass-type Mythical Pokémon. It is referred to as the guardian of forests, protecting and nourishing them as it travels through time.
Celebi shares a special connection with the Ilex Forest in Johto, having the Ilex Forest shrine to honor. It also shares a connection to the Unown. A GS Ball can be found when the Unown have been unlocked in the Sevii Island's Tanoby Chambers that when brought to the Ilex Forest Shrine will draw out Celebi.
Diancie
Diancie is a Rock/Fairy-type Mythical Pokémon. It is said to be the result of a Carbink that underwent a mutation. It can create diamonds to protect itself. It is the only Mythical Pokémon with the ability to Mega Evolve, which allows it to transform into Mega Diancie.
It was discovered by accident in what is now Diamond Dive when coal miners near Cherrygrove City stumbled upon it while following a surprise seam of diamonds. In its surprise it collapsed a river into the mines leaving them partially submerged and generally unusable.
Sevii Islands
Manaphy and Phione
Manaphy is a Water-type Mythical Pokémon, and Phione is a Water-type Pokémon. Manaphy are born on cold seafloors, also swimming great distances to return to their birthplace, and are born with a wondrous power to bond with any kind of Pokémon. Phione live in warm seas, using the inflation sac on their heads to search for food and to drift in packs, always returning to the place of their birth. Together, these two Pokémon species make up a Mythical duo of a parent and child.
Manaphy and Phione have the unique ability among Mythical Pokémon to breed with Ditto in captivity to produce Phione. Phione cannot, however, evolve into Manaphy. A Manaphy Egg can be found at the bottom of an underwater cave off the shore of the Sevii Islands. The exact location of the cave is pinpointed on the Empty Sea Map.
Mew
Mew is a Psychic-type Mythical Pokémon. It is believed to contain the genetic codes of all Pokémon in its DNA. Initially thought to be extinct, a scientific team eventually reported sightings of it in Guyana. Mewtwo was created after a series of experiments based on Mew, and is thus considered to be part of a Legendary duo with it.
It has been known to travel widely but, does consider an obscure, remote island near the Sevii Islands, Faraway Island its home. An Old Sea Map can be used to travel to the island.
Volcanion
Volcanion is a Fire/Water-type Mythical Pokémon. It uses steam from arms on its back to disappear in fog and blow away mountains. It lives in mountains uninhabited by humans. According to the editor of the Lumiose Press, Volcanion may have an organ unique to it inside its body that is hot enough to instantly vaporize water into steam to use in attacks. There is also a report that suggests that Volcanion may have used its power to destroy a mountain range where Kalos was founded.
It moves between many valcanoes, often causing them to become more active than before. It has most recently been sighted atop Mt. Ember.
Unova
Victini
Victini is a Psychic/Fire-type Mythical Pokémon. It is said that this Pokémon brings victory and that Trainers with Victini always win, regardless of the type of encounter. It creates an unlimited supply of energy inside its body, which it shares with those who touch it. When it shares the energy it creates, that being's entire body will be overflowing with power.
A rich gentleman is credited with building a lighthouse on Liberty Garden in Unova to house and protect it from those who wish to exploit it, like Team Rocket. The Liberty Sea Map allowed players to travel to Liberty Garden.
Tao Trio
Zekrom, an Electric/Dragon-Type and Reshiram, a Fire/Dragon-Type represent balance through the aspects of Yin and Yang, respectively. Originally, they were a single dragon that helped found the Unova region's nation, but fighting between the two brothers who founded the nation split them into two halves. Despite this, the two Pokémon do not willingly fight each other. In the aftermath they sealed themselves into seemingly inert stones in the remote-to-Unova region of the Sevii Islands, specifically Dotted Hole and Mt. Ember respectively. The ancient Embedded Tower on Johto's Route 47 also seems to be tied to the stones. The reason for these ties to regions outside of the Unova region, where they are well documented in local legend, is currently lost to time.
Kyurem, an Ice/Dragon-type is related to Reshiram and Zekrom and represents wuji, which is the absence of yin and yang. A geneticist in the Pewter Museum, can use his research to fuse or unfuse Kyurem with Reshiram or Zekrom into White Kyurem or Black Kyurem, respectively.
Psuedo Legendaries
Sometimes tied in with the other legendaries are a class of Pokemon known as Psuedo Legendaries. These Pokemon are all the end of 3-stage evolutions families, are in the "Slow" exp group, and have a Base stat Total of exactly 600. In addition, 6 of the 8 psuedo legendaries are Part Dragon-type. The Psuedo Legends are: