The Pokémon Lyogre does not exist. The Pokémon Kyogre exists but cannot be caught in Pokémon Ruby. Kyogre can only be caught in the Cave of Origin in Pokémon Sapphire. To catch Kyogre, assemble a strong team of Pokémon, acquire Pokéballs and enter Sootopolis City to access the Cave of Origin.
- Assemble a strong team of Pokémon
In order to get to the Cave of Origin in Pokémon Sapphire, you will need to create a team of Pokémon that is strong enough to defeat seven gym leaders scattered across the Hoenn region. Having your Pokémon learn moves that can inflict status condition such as paralysis, a burn, poison or sleep will significantly improve your chances of catching Kyogre. Additionally, the False Swipe move will inflict damage to the opposing Pokémon, always leaving it with at least one health point and thus never causing it to faint.
- Acquire Pokéballs
In Pokémon Sapphire there are several types of Pokéballs. The most efficient Pokéballs to catch Kyogre are Ultra Balls and the Master Ball. Ultra Balls are easily obtained from Mossdeep City for 1200 Pokédollars, so obtain as many as possible. The Master Ball guarantees the capture of any Pokémon target, and can be found in the Team Aqua hideout in story mode.
- Head to Sootopolis City
After following the story mode and successfully defeating seven of the eight gym leaders in the game, you will receive the Blue Orb and gain access to a new area called Sootopolis City. Upon arrival you will be greeted by Steven and the Eighth Gym Leader who will lead you to the Cave of Origin. Follow the cave to the end and you will encounter Kyogre. First, use one of your Pokémon to inflict Kyogre with a status condition. After this, use another one of your Pokémon to weaken Kyogre until its health is almost depleted. Finally, throw either the Ultra Ball or the Master Ball at Kyogre.