Instructions
Complete the game up to the point of Cinnabar Island. After defeating Gym Leader Blaine, enter the Pokemon Center. Bill will be waiting for you, and ask if you would assist in a sidequest on One Island. Say yes, and he will give you the "Tri-Island Pass," allowing you to go to the first three of the Sevii Islands.
Assist with the rescue of Estelle by completing the quests on the first three islands. You will then be able to continue the game from the point of Cinnabar Island, going on to defeat the Elite Four. After doing so, you will receive the National Pokedex. With this, you may acquire the next pass.
Go to One Island's Pokemon Center. A man named Celio will be waiting for you and upgrades your Tri-Island Pass to a "Rainbow Pass,: allowing you access to all seven of the Sevii Islands. Several other quests on each island are made available to you.
Warp to Eight Island using the Mysticticket, acquirable at a Nintendo sponsored event, or by using a GS/Action Replay.
Catch or defeat Ho-Oh and Lugia on Eight Island. As there are no trainers or quests on this island, you may then continue on to Nine Island using the item Oldseamap, obtainable with the GS/Action Replay.
Press the A button while standing in front of the rock in the triangle at the top of the stairs. The rock moves, and you must follow it and press A until it moves to the top of the formation. Pressing A once more causes the legendary Pokemon Deoxys to attack, at which point you may capture it.