You can not come back, trust me i tried
But you can still find them and catch them in the grass if you use max repel and search the grass about 20-30 times. But make sure you have a lot of poke, great, or ultra balls.
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If Moltres,Zapdos or articuno runs away you need to use action replay to get them back
If you defeated Zapdos, you can never get him again, unless if you trade from Pokemon LeafGreen or FireRed. If you did defeat him, you should have saved the game before pressing the button, A, on it. That way, if you defeat him, you can just turn off the game and turn it back on and you will find Zapdos still there! ed by: QWERTY
Before you battle, make sure you safe because if you kill the articuno it won't come back. attack the Articuno until it has low HP. Then use a move that puts it to sleep or parlyzes it. This will increase your chances of catching it.
zapdos: at flying city go to the storage tower and when the girl kisses you on the LIPS the delivery man see`s you and tells you to look in his new box in it is HM 10 thunder then go out and use it and zapdos will appear. moltres: if you have your heat (3rd) badge and have the HM07 splash use it in the gym and when your screen is all red you will battle moltres! articuno: if you have your blizzard (1st) badge go back to snowland town and click on the left bottom igloo inside is articuno. mewtwo: you cant battle it. if you have room in your party and have mew give it a clone stone and mewtwo will be in your party! mew: you cant get it unless you have friends who have it on games like diamond, pearl and other games with pokecentres you need to trade it . raikou: go to your home town house and if you have the HM10 thunder and you have plant by your house use thunder and raikou will appear but then goes into the town sign. entei: in victory volcano pickup an E unown a N unown a T unown an E unown and an I unown then go to the top of victory volcano and in two stones you will battle ENTEI. selucian: in diblo lake cavern when got zapdos, moltres and articuno. lugia: their is no way to get it in flying if you like to have one by trade on their screen bit of lugia will be blank you can trade only when got zapdos, moltres and articuno. ho-oh: i forgot this one but try looking on www.helponfly.com. im sorry that's how much i know soz.
go in front of it and save the game and ever time u kill it turn off your ds and turn it back on