After you have defeated Suicune (or any of the legendary dogs for that matter), theres no going back. You have killed them, if you turn off your game and had not saved after killing Suicune, then you are fine. To make sure you don't kill him, a good move would be to get a Scyther, and make sure they know false swipe, since that will always leave at least 1 HP, then try to set them to sleep, and use an ultra ball. DON'T USE YOUR MASTER BALL. Suicune will not flee unlike Raikou and Entei, so save before you battle him and get him using an Ultra Ball. You could use your master ball on the Lugia (Level 60) or use it on either Entei or Raikou. I've also heard that you can get Ho-oh who will be at a high level.
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The most important pokemon to catch in any game is its mascot, in this case Suicune.
Raikou, Entei, Suicune, Ho-oh, Lugia and Celebi.
To complete the storyline you have to beat the Elite 4 To really beat the game you have to defeat Red on Mt.Silver To become a Pokemon master though, you have to catch all 251 Pokemon available in Crystal version
in any version you need a masterball