There are three pokemon that are hidden in the game.The pokemon are Zapdos, Mortles, and Artincuno.
Zapdos can be found in the Power Plant by Cerulean City. Go on route 9,the area near the Rock Tunnel which you needed Flash for. Make sure you have the SURF abilty. Once you have surf go to the area where Route 9 ends. Go to the water and use surf. Keep going down and you'll see a opening where the rocks brek to open land, go on that and you'll see a big building. Go in there a keep walking around untill you see a bird pokemon standing there. Save your game and then fight the bird. Capture it, then its on too Fuchsia City!
If you have fly go to the Fuchsia City gate on the left. You'll see a few little jumpable cliffs. Go to the edge of the water and use surf. Keep going left and you should see some islands. Go in the cave that on the islands. You must have strength to get this next bird. Once in the cave find you way through the cave pushing all the rocks down the holes. This is important because you need to stop the curant flow down below int he cave. Once you find you way to another bird pokemon, do the same as before. This is going to be Articuno.
The final pokemon is Moltres, who an be found once you have all eight badges. After you have all the badges go to Victory Road at the Pokemon League. Make you way through the cave and you should see another bird pokemon. Repeat the same steps as you did for the outher Pokemon.