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You will get Kyogre in Undersea Express, so get the ticket after defeating Red in Mt. Silver ;) And same with Groudon, you will be able to fight against it when you defeat the Saturn team in Dragons Den ;)
Lugia is in Whirl Islands (appears when you have silver wing, just 1 cave is for Lugia!) Regi's and Groudon are catchable in Dragons Den after defeating Silver and the other guy, in this secound entrance), Raikou and Entei are random encounters in Johto, Jirachi is in Dark Cave. No plan what to...