Location: Cave of Origin

The main Legendary Pokémon in the games are found within the Cave of Origin as you go through the story. After being awakened on the Seafloor Cavern, the legends will be found in the deepest part of the Cave of Origin. When you battle them, they will Primal Revert to their Primal forms automatically. As such, when captured, they come holding their orbs. Groudon is found in Omega Ruby and Kyogre is found in Alpha Sapphire. They don't have their orbs straight away, but you get given them immediately after the battle

Groudon Level 45

OT: Yours ID: Yours Ability: Drought Hold Item: None

??? Nature. Date of Receiving Cave of Origin. Caught at Lv. 45

Lava Plume Rest Earthquake Precipice Blades

Kyogre Level 45

OT: Yours ID: Yours Ability: Drizzle Hold Item: None

??? Nature. Date of Receiving Cave of Origin. Caught at Lv. 45

Body Slam Aqua Ring Ice Beam Origin Pulse

Location: Desert Ruins

The Regi trio have got the same legwork to activate. Before the three locations become available to you you must have a Relicanth and Wailord as well as a Pokemon with Dig and Dive. On Route 134 you must take the correct path through the currents to the patch of water you can Dive in. Once below folow the path up to the Braille inscription and resurface. Go to the next inscription and use Dig. Make Relicanth the 1st of your party and Wailord the 6th, then read that inscription. Three earthquakes will trigger and open passages on each respective route.
Regirock is found in the Desert Tomb, which is at the bottom of the desert in Route 111. Scribed on the walls inside is a message like the ones on Route 134: go right twice, down twice (best use the D-Pad for this) and then use Strength and the door to Regirock should appear. It's at Level 40, so be prepared.

Regirock Level 40

OT: Yours ID: Yours Ability: Clear Body Hold Item: None

??? Nature. Date of Receiving Desert Ruins. Caught at Lv. 40

Bulldoze Curse Ancient Power Iron Defense

Location: Island Cave

The Regi trio have got the same legwork to activate. Before the three locations become available to you you must have a Relicanth and Wailord as well as a Pokemon with Dig and Dive. On Route 134 you must take the correct path through the currents to the patch of water you can Dive in. Once below folow the path up to the Braille inscription and resurface. Go to the next inscription and use Dig. Make Relicanth the 1st of your party and Wailord the 6th, then read that inscription. Three earthquakes will trigger and open passages on each respective route.
Regice is hiding out in Island Cave, which is on a small reef on the west part Route 105, requiring Surf to gain access. Once inside, you will find a message in braille telling you to wait. After two minutes the door opens and Regice can be fought.

Regice Level 40

OT: Yours ID: Yours Ability: Clear Body Hold Item: None

??? Nature. Date of Receiving Island Cave. Caught at Lv. 40

Bulldoze Curse Ancient Power Amnesia

Location: Ancient Tomb

The Regi trio have got the same legwork to activate. Before the three locations become available to you you must have a Relicanth and Wailord as well as a Pokemon with Dig and Dive. On Route 134 you must take the correct path through the currents to the patch of water you can Dive in. Once below folow the path up to the Braille inscription and resurface. Go to the next inscription and use Dig. Make Relicanth the 1st of your party and Wailord the 6th, then read that inscription. Three earthquakes will trigger and open passages on each respective route.
Registeel is the last of the three, found west of Lilycove in Route 120's Ancient Tomb. The answer to this riddle to is use Fly in the middle of the room. Doing so will expose Registeel.

Registeel Level 40

OT: Yours ID: Yours Ability: Clear Body Hold Item: None

??? Nature. Date of Receiving Ancient Tomb. Caught at Lv. 40

Curse Ancient Power Iron Defense Amnesia

Location: Sky Pillar

As you progress through the Delta Episode, you will eventually come to a climax which has you and Zinnia reach the top of Sky Pillar and awaken Rayquaza. Rayquaza eats your meteorite and refuses to accept Zinnia as its protector, and instead wishes to challenge you. It's at Level 70 and requires capture to proceed. It also will require you to send a Pokémon back to your box from your team. Immediately after capturing it, Zinnia teaches it Dragon Ascent and challenges you to a battle. It can Mega Evolve without holding a Mega Stone, but needs to know Dragon Ascent to do so.

Rayquaza Level 70

OT: Yours ID: Yours Ability: Air Lock Hold Item: None

??? Nature. Date of Receiving Sky Pillar. Caught at Lv. 70

Extreme Speed Dragon Pulse Dragon Dance Dragon Ascent

Location: Sky Pillar

After defeating Zinnia with Rayquaza, you will then go up in space in order to defeat the asteroid which is heading towards the planet. Doing so has Rayquaza Mega Evolve and destroy the asteroid. However, from the remnants comes the black triangle which opens up and unleashes Deoxys, who challenges you. It is at Level 80 and your Rayquaza starts out Mega Evolved, so you cannot Mega Evolve any other Pokémon in the battle.

Deoxys Level 80

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Sky Pillar. Caught at Lv. 80

Cosmic Power Recover Psycho Boost Hyper Beam

Location: Island Cave

Once you have the three Regis, Regirock, Regice and Registeel, you can unlock Regigigas. The method to get this is rather complicated. In Pacifidlog Town, in the north-eastern house, a girl will tell you stories her grandfather told her. At random, she will tell you a part of the story about how to get Regigigas. This involves location and the other features. Take all three of the Pokémon to the Island Cave during the day, and make Regice hold a frozen item such as CasteliaCone, Snowball or Never-Melt Ice, and have Regice have a nickname, and Regigigas will challenge you

Regigigas Level 50

OT: Yours ID: Yours Ability: Slow Start Hold Item: None

??? Nature. Date of Receiving Island Cave. Caught at Lv. 50

Foresight Revenge Wide Guard Zen Headbutt

Location: Sea Mauville

After you have dealt with Primal Groudon/Kyogre, when you go to Sea Mauville, you can hunt for the Scanner in the basement. When found, if you take it to Captain Stern in Slateport City, he will give you a key item. This item is the Clear Bell in Omega Ruby and the Tidal Bell in Alpha Sapphire. Take the bells to Sea Mauville and they will start to resonate, on the deck in Omega Ruby and in the underwate basement in Alpha Sapphire. This causes a portal to appear. Interact with it and Ho-Oh will appear in Omega Ruby, and Lugia will appear in Alpha Sapphire.

Ho-Oh Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: Sacred Ash

??? Nature. Date of Receiving Sea Mauville. Caught at Lv. 50

Sunny Day Fire Blast Sacred Fire Punishment

Lugia Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Sea Mauville. Caught at Lv. 50

Rain Dance Hydro Pump Aeroblast Punishment

Location: Scorched Slab

After you have dealt with Primal Groudon/Kyogre, when you go into Scorched Slab, you will encounter Flannery who exclaims that she is looking for a Pokémon that is said to be found within it. Traverse to the bottom of the cave and you will find another portal. Interact with the portal and you will get challenged by Heatran

Heatran Level 50

OT: Yours ID: Yours Ability: Flash Fire Hold Item: None

??? Nature. Date of Receiving Scorched Slab. Caught at Lv. 50

Metal Sound Crunch Scary Face Lava Plume

Location: Southern Island

After you have received the Eon Ticket through event or StreetPass, you can speak to Norman in the Petalburg City Gym. He will explain the ticket and take you to the ferry to go to Southern Island. When there, you will find Latias in Omega Ruby or Latios in Alpha Sapphire, opposite one to the one you were given earlier in the game. After capture, you will find the Soul Dew on the ground.

Latias Level 30

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Southern Island. Caught at Lv. 30

Heal Pulse Dragon Breath Mist Ball Psycho Shift

Latios Level 30

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Southern Island. Caught at Lv. 30

Heal Pulse Dragon Breath Luster Purge Psycho Shift

Location: Nameless Cavern (Near Sootopolis City)
Additional Requirements: Three Pokémon with max Happiness on team

When Soaring around by Sootopolis City, you will discover a very small area called the Nameless Cavern. Inside the cave in the area, you will note a familiar pattern on the ground and a portal. Interact with the portal and Uxie, Mesprit or Azelf will challenge you. Uxie can be found between 20:00 and 21:00, Azelf can be found between 21:00 and 03:59 and Mesprit can be found between 04:00 and 19:59. Note: Times are still being finalised

Uxie Level 50

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Nameless Cavern. Caught at Lv. 50

Yawn Future Sight Amnesia Extrasensory

Mesprit Level 50

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Nameless Cavern. Caught at Lv. 50

Lucky Chant Future Sight Charm Extrasensory

Azelf Level 50

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Nameless Cavern. Caught at Lv. 50

Uproar Future Sight Nasty Plot Extrasensory

Location: Soaring in the Sky (South of Dewford Town)
Additional Requirements: Azelf, Mesprit & Uxie in your team

If you have Azelf, Uxie and Mesprit in your team while you're Soaring in the Sky, when you near Dewford Town, you will discover a large tear in the Space-Time Continuum. As you approach the tear, you will be asked if you wish to enter. If you do, then Palkia will attack in Omega Ruby, and Dialga will attack in Alpha Sapphire

Palkia Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Earth Power Aura Sphere Spacial Rend Hydro Pump

Dialga Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Aura Sphere Iron Tail Roar of Time Flash Cannon

Location: Soaring in the Sky (South of Dewford Town)
Additional Requirements: Dialga & Palkia in your team

If you return to the same area as above with Dialga and Palkia in your team while you're Soaring, then the tear in the space-time continuum will return. Fly into it and this time you will be challenged by Giratina

Giratina Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Aura Sphere Shadow Claw Shadow Force Hex

Location: Pathless Plain (Near Pacifidlog Town)
Additional Requirements: Three Pokémon with max Effort Values on your team

When Soaring around by Pacifidlog Town, you will discover a large island called the Pathless Plain. When you land, you will find a small path to a peninsula where a portal is standing. Interact with the portal and Virizion, Terrakion and then Cobalion will challenge you. Cobalion can be captured on Sundays, Wednesdays and Fridays, Terrakion can be captured on Tuesdays and Saturdays and Virizion can be captured on Mondays and Thursdays

Virizion Level 50

OT: Yours ID: Yours Ability: Justified Hold Item: None

??? Nature. Date of Receiving Pathless Plain. Caught at Lv. 50

Retaliate Giga Drain Sacred Sword Swords Dance

Terrakion Level 50

OT: Yours ID: Yours Ability: Justified Hold Item: None

??? Nature. Date of Receiving Pathless Plain. Caught at Lv. 50

Retaliate Rock Slide Sacred Sword Swords Dance

Cobalion Level 50

OT: Yours ID: Yours Ability: Justified Hold Item: None

??? Nature. Date of Receiving Pathless Plain. Caught at Lv. 50

Retaliate Iron Head Sacred Sword Swords Dance

Location: Fabled Cave (South-east of Mauville City)
Additional Requirements: Have a Level 100 Pokémon on your team

When Soaring around, you may discover a small area near Mauville City which has a star above it. This is the Fabled Cave and inside the cave you will find another portal. In it, you will encounter Reshiram in Omega Ruby or Zekrom in Alpha Sapphire.

Reshiram Level 50

OT: Yours ID: Yours Ability: Turboblaze Hold Item: None

??? Nature. Date of Receiving Fabled Cave. Caught at Lv. 50

Dragon Breath Slash Extrasensory Fusion Flare

Zekrom Level 50

OT: Yours ID: Yours Ability: Teravolt Hold Item: None

??? Nature. Date of Receiving Fabled Cave. Caught at Lv. 50

Dragon Breath Slash Zen Headbutt Fusion Bolt

Location: Gnarled Den (Near Fallarbor Town)
Additional Requirements: Reshiram & Zekrom on team

When Soaring in the Sky, if you have both Reshiram and Zekrom in your team, then a new area will open up. This area can only be accessed when both Pokémon are in your team. This area is located behind Mt. Chimney and is known as the Gnarled Den. Inside, you will find a portal that has Kyurem in. In addition to that, if you use the Dowsing Machine, you will find the DNA Splicers in the cave

Kyurem Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Gnarled Den. Caught at Lv. 50

Dragon Breath Slash Scary Face Glaciate

Location: Trackless Forest (Near Rustboro City)
Additional Requirements: Lugia or Ho-Oh on team

When Soaring in the Sky, if you have Lugia or Ho-Oh in your team, then a new area will open up. This area can only be accessed when one of the Pokémon is in your team. This area is located east of Rustboro City and is a small forest. In there, you will find a portal which has Raikou, Entei or Suicune in. For Raikou, the time needs to be between 00 and 20 minutes past the hour, for Entei the time needs to be between 20 and 40 minutes past the hour and for Suicune, the time needs to be between 40 and 00 minutes past the hour.

Raikou Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Trackless Forest. Caught at Lv. 50

Spark Reflect Crunch Thunder Fang

Entei Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Trackless Forest. Caught at Lv. 50

Stomp Flamethrower Swagger Fire Fang

Suicune Level 50

OT: Yours ID: Yours Ability: Pressure Hold Item: None

??? Nature. Date of Receiving Trackless Forest. Caught at Lv. 50

Aurora Beam Mist Mirror Coat Ice Fang

Location: Soaring in the Sky (Near Fortree City)
Additional Requirements: Castform on team

When Soaring in the Sky, if you have a Castform on your team, then a thunder cloud will appear over Fortree City. If you get close to it, you will get the option to fly in where you'll be able to battle the Pokémon Tornadus in Omega Ruby or Thundurus in Alpha Sapphire

Tornadus Level 50

OT: Yours ID: Yours Ability: Prankster Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Extrasensory Agility Air Slash Crunch

Thundurus Level 50

OT: Yours ID: Yours Ability: Prankster Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Heal Block Agility Discharge Crunch

Location: Soaring in the Sky (Near Fortree City)
Additional Requirements: Tornadus & Thundurus on team

When Soaring in the Sky, if you have both Tornadus & Thundurus in your team, then a thunder cloud will appear over Fortree City. If you get close to it, you will get the option to fly in where you'll be able to battle the Pokémon Landorus

Landorus Level 50

OT: Yours ID: Yours Ability: Sand Force Hold Item: None

??? Nature. Date of Receiving Soaring in the Sky. Caught at Lv. 50

Extrasensory Swords Dance Earth Power Rock Slide

Location: Crescent Isle
Additional Requirements: Random Daily Mirage Island

At some point, with the daily Mirage Spot change, an island will appear south of Ever Grande City. On this island, you will find a portal that gives you access to Cresselia as well as hidden items. The chances of this island appearing are slim, but you can improve chances by going online and receiving Mirage Spots

Cresselia Level 50

OT: Yours ID: Yours Ability: Levitate Hold Item: None

??? Nature. Date of Receiving Crescent Isle. Caught at Lv. 50

Mist Aurora Beam Future Sight Slash