Instructions
Finish the main storyline by collecting all 16 badges, defeating the Elite Four and defeating your rival at the end of the game. After the credits roll, you can continue playing your game.
Fly to Pallet Town and talk to Professor Oak in his lab. He will congratulate you on beating your rival by offering you one of the Starting Pokemon from the Kanto region. Choose whichever one you prefer.
Fly to New Bark Town and talk to Professor Elm. He will congratulate you on defeating the Elite Four and give you the S.S. Ticket. Fly to Olivine City and walk to the port to meet up with Professor Oak. Talk to Oak to obtain the National Pokedex.
Travel to Mr. Pokemon's house in the northern part of Route 30. Talk to Mr. Pokemon to receive the Blue Orb in "Pokemon HeartGold" or the Red Orb in "Pokemon SoulSilver." With these key items in hand, you can now encounter either Groudon or Kyogre, depending on your version of the game.
Travel through Route 45 to reach the Embedded Tower at the top of a climbable wall. Make your way through the path of the Embedded Tower to encounter either Groudon or Kyogre at the end of the path.
Battle Groudon or Kyogre to weaken the Pokemon, and then throw a heavy-duty Poke Ball to capture it. Groudon and Kyogre are at level 50 when you encounter them, so select your highest-level Pokemon to send into battle.