Location: Cave of Origin

Method:
At the end of your version's evil team's plotline, you will have a chance to fight the Pokemon they were after. In Sapphire this is Kyogre, who summons instant and permanent rain into battle. It has a terrific STAB boosted Hydro Pump move that can be buffed by Calm Mind (moreso in the rain) as well as the strong Ice Beam moves to seriously injure your Grass- and Flying-types.In Ruby this is Groudon, who summons instant and permanent harsh sunlight into battle. Its Fire Blast technique is boosted by weather and Earthquake is a mighty STAB that gets buffed by Bulk Up, and Slash which has a high chance of landing a critical hit.

Location: Desert Tomb

Method:
This generation's legendary trio has a bit more legwork involved with obtaining. 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 sandstormy desert in Route 111. Scribed on the walls inside is a message like the ones on Route 134: go right twice, down twice and then use Strength and the door to Regirock should appear. It's at Level 40, so be prepared.

Location: Island Cave

Method:
This generation's legendary trio has a bit more legwork involved with obtaining. 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 Route 105. Once inside, you will find a message in braille telling you to wait. After two minutes the door opens and Regice can be fought. Another Level 40 Pokemon, you should avoid its Icy Wind move.

Location: Ancient Tomb

Method:
This generation's legendary trio has a bit more legwork involved with obtaining. 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. This one is at Level 40 as well.

Location: Sky Pillar

Method:
High above Sky Pillar after you earn the title of Champion waits Rayquaza, who instantly negates all weather in battle and has a mighty line up of moves. Two strong and useful STABS, a recovery move, and a priority attack make for a battle that demands only your best. It can Rest off status, remember, so bright a couple dozen of your favourite Pokeballs and a well planned team.

Location: Southern Island

Method:
In Ruby, you can find Latias and Sapphire you can find Latios. They can be found on the Southern Island if the player obtains an Eon Ticket through an e-Reader card (distributed through Nintendo Power) or by mixing records with someone who has it. Norman, your father, will give you the ticket and tell you to visit Lilycove City where Mr. Briney will ferry you to the secret island. There you can find the legendary dragons at a higher level in a secret forest. Be careful though as it has some strong moves and is holding a Soul Dew, which increases its Special Attack and Special Defense.

Method:
After you beat the Pokemon League, these Pokemon roam around Hoenn in the fashion of the Legendary Dogs from Gold and Silver. They flee the first turn and appear elsewhere on the map. You must trap them with a move like Spider Web to have a proper fight. Latios is in Ruby and Latias is in Sapphire. The former is more offensive oriented, and the latter is more defensive, so choose your Pokemon for battle accordingly.