The following Legendary Pokémon are available in Eternal Order:

-Entei
-Raikou
-Suicune
-Azelf
-Mesprit
-Uxie
-Phione
-Manaphy
-Jirachi
-Celebi
-Type:Null
-Silvally
-Genesect
-Shaymin
-Xerneas
-Yveltal
-Zygarde
-Registeel
-Regirock
-Regice
-Regigigas
-Darkrai
-Cresselia
-Deoxys
-Mewtwo
-Kyurem
-Zekrom
-Reshiram
-Dialga
-Palkia
-Giratina
-Arceus

How to get them:

-Entei, Raikou & Suicune
They become available once the Pokémon League is opened.
Entei can be fought in Mt. Opal.
Raikou can be fought in Iron Corps.
Suicune can be fought in Mt. Uller's Base.

-Azelf, Mesprit & Uxie

They become available once the Pokémon League is beaten.
Azelf can be fought in the Cavern of Willpower.
Mesprit can be fought in the Cavern of Emotion.
Uxie can be fought in the Cavern of Knowledge.

-Phione and Manaphy

Manaphy can be fought inside an underwater cave in Mt. Uller's Base.
Beating Manaphy will let you take a Phione egg. Phione evolves into Manaphy at lvl.
60.

-Jirachi
Can be fought inside the Basalt Cave if you have a Wish Tag.

-Celebi
Can be fought in the Fenlan Woods by getting a GS Ball from Gourien City.
To get the GS Ball, you must first get a key from Saphyrix Town.
-Type:Null and Silvally
Can be obtained after completing the final ranger mission.

-Genesect
Can be fought inside the Desert Ruins after obtaining the Drive Detector inside the
player's home
and then talking to a scientist inside Solaris Corps.

-Shaymin
Can be fought inside the Peridot Cave.

-Xerneas
Can be fought in the Gourien Forest after obtaining the Azure Onyx.
The Azure Onyx can be obtained inside the Opal Altar after beating the Pokémon
League.

-Yveltal
Can be fought in Mt. Uller after obtaining the Crimson Onyx.
The Crimson Onyx can be obtained inside the Opal Altar after beating the Pokémon
League.

-Zygarde
Can be fought at the Opal Altar after obtaining the Jade Onyx and defeating Xerneas
& Yveltal.
The Jade Onyx can be obtained after the final fight with Zenon.

-Registeel, Regirock & Regice

Can be fought after checking out the Regigigas statue inside the underwater cave
from Arctic Island.
Registeel can be fought in a cave in Sprucefield Road.
Regirock can be fought in a cave in Adamantine Desert.
Regice can be fought in a cave in Crystal Valley.

-Regigigas
Can be fought inside the Sealed Chamber after beating the 3 Regis.

-Cresselia
Can be fought after obtaining the Lunar Wing and sleeping at the Corall Hotel.
The Lunar Wing can be found in the Oceanus Trench.

-Darkai
Can be fought after obtaining the Lunar Claw and sleeping at the Corall Hotel.
The Lunar Claw can be found in Ashen Wastelands.

-Deoxys
Can be fought when entering the Research Department inside Renoe City.

-Mewtwo
Can be fought inside the Bronze Corps after getting Bronze Key from the Basalt
Cave.

-Kyurem
Can be fought inside the Frozen Forest near Follour City after defeating the Elite
Four.
The DNA Splicers can be obtained from a scientist inside Renoe City.

-Zekrom
Can be fought in the Black City after defeating the Chosen Ones.
-Reshiram
Can be fought in the White Forest after defeating the Chosen Ones.

-Dialga
Can be fought inside the Hall of Origin after defeating Arceus.

-Palkia
Can be fought inside the Hall of Origin after defeating Arceus.

-Giratina
Can be fought inside the Phantom Cave.

-Arceus
Can be fought inside the Hall of Origin if the player has all the plates.